‘99 YZ400F Rebuild

Perky
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Edited Date/Time 10/18/2023 9:00am

IMG 6057 0Hey all! Excited to be doing one of these after a year of quietly rebuilding a RM125.

I just picked up a 1999 YZ400F as part of a package deal from a gentleman in Alamosa, CO. My heart will forever lie with two-strokes, but the story of the YZ400F was my one exception.

Any info you fine folks are able to share would be greatly appreciated, (especially since four bangers are not my forte) and check back in to see its return to former glory!

J.P.

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sandman768
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10/18/2023 4:39am

Awesome… I”m all 2stroke as well. I have thought about picking up an old 4t to learn how to rebuild them…

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Perky
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3/15/2026 8:21am Edited Date/Time 3/15/2026 8:21am

So after two and a half years of trucking this thing around for two moves, I finally got my garage set up (enough) and some time to get to tearing this thing down.


Shockingly, the oil looks fresh. Could’ve been changed before it was put up, but a sigh of relief for sure since I was worried about the corrosion inside the frame tubes where oil is kept on these things.


Same story with the coolant. Looks fresh like it was just changed before put up. The carb didn’t haven’t any debris either despite the air filter looking the way it does.


As soon as I can get the motor out of the frame, she’s off to Miller ATV & Cycle in Virginia for a full rebuild. I figured after sitting on it this long, I’ll have someone else get the motor back in working order while I teach myself how to rebuild the suspension and prep and paint the frame.

IMG 5023 1IMG 5065 5IMG 5072 3IMG 5184 2.jpeg?VersionId=dlylHWLym7xNwiUAjeiFkdi

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Perky
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3/21/2026 4:47pm

I need some suggestions - the main frame bolt is seized in the frame. No amount of WD40, heat or mallet-ing will get this thing to break loose. Is there an anti-seize compound you can suggest?

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sandman768
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3/21/2026 5:57pm

I would remove all other engine mounting bolts and linkage from swing arm…lay bike on side and soak swingarm bolt with Kroll and/ or PBblaster,…wd-40 is not an effective lubricant for frozen bolts….you can also make a mixture of acetone and ATF…..Be patient…soak each side, laying bike on its side…you want to try and save the bolt, and keep the hammering to a minimum….after soaking for a few days on each side, then try heating the bolt, engine casing/ collars, use a long tapered punch that fits inside the bolt, use large hammer….

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The Shop

Jason358
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3/22/2026 10:52am

Everything sandman said above is 100% solid advice. Kroil penetrating oil in the orange can is the good stuff. The only thing I’ll add to what was said is use a bit of heat to get the penetrating oil to draw into the places it needs to be a little better/easier. I’ve had to set entire frames/engines in a press and do the heat/oil/pressure thing for days on end. It will come out it just takes some patience sometimes. Good luck! 

 

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3/22/2026 12:26pm

Heat guns better then a torch on this one.

450exc115
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3/23/2026 5:48am

Instead of a hammer and punch use an air chisel with a blunt ended attachment after heat and penetrant.  

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BoxcarWilly
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3/23/2026 10:37am

Air hammer will get that out in 5 seconds. 

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Perky
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3/28/2026 2:17pm

Following @sandman768’s advice… day 1/3 after a long week of the flu.

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sandman768
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3/28/2026 7:07pm
Perky wrote:
Following @sandman768’s advice… day 1/3 after a long week of the flu.

Following @sandman768’s advice… day 1/3 after a long week of the flu.

IMG 5691 1

Thats it, just be patient,…it will come out…

sandman768
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3/29/2026 5:09am

Side note: hit that front sprocket nut with an impact gun while chain still on bike, probably apply some heat / PBlaster to that nut as well…this roach required the same treatment for every bolt….IMG 0014 2.jpeg?VersionId=lBu9aKImyWpl4TOILnUN3M rNiMswx

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Timo
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3/29/2026 8:46am

Everyone knows about torquing sprocket bolts, but we really need to push the grease your pivot and axle bolts more 😅.

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Perky
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3/30/2026 5:22pm

Hell yeah @sandman768! 10min of 1200° F and that bolt slid out as easy as a hot knife through butter!

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Perky
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3/30/2026 8:15pm

Out and off to Miller ATV & Cycle!

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BoxcarWilly
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3/31/2026 6:40am

You're missing out on most of the fun shipping that out instead of doing it yourself!

Do you have an idea of what the engine needs? 

Perky
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3/31/2026 4:19pm

@BoxcarWilly I know - I bought it for $100 a few years ago and if I’m lucky I’ll get it together in time for this season. Really weak compression and it likely hasn’t run in the past decade.

While the engine is out I plan on teaching myself how to rebuild the suspension, so there’s still some fun to be had!

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motorick5052
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IMG 9598 3.jpeg?VersionId=RaY8Cz2ML9mK9aWldLYDzXzz7XkWf7GIMG 0848 1IMG 9602 3

Hey Perky! 
I hope your build goes really well and you get the bike restored in a way that will make all your wildest dreams come true! 🤪

My brother and I had em and we LOVED them! I had a 98 & 99 400, a 2000 & two 2002 426’s and they were all fun/fast bikes, once you got the feel for the thumper and came to terms with the compression braking! 
(First pic is my brother & I, amateur Sunday, AMA Arenacross @ Lazy E Arena, Guthrie Oklahoma. Second two are me, then my brother, on different jumps at our local track, the infamous Midwest track, Motorcycle Raceway in Oklahoma City! Known far and wide by MX’ers all around this part of the country as … 59th & Douglas! 😝)

One old trick I would pass along during the engine rebuild that you might consider? IF you’d care to avoid the starting drill that the compression lever was famous for, consider having the exhaust cam from the 2003 YZ450f  installed in the 1999 YZ400! The 2003 YZ450 cam with the auto-decompression built into the cam, is a direct / drop-in replacement and will eliminate the ridiculous starting drill, as well as avoiding having the compression lever on the bar! (And the associated damage that could result from unintentional engagement!)

Keep the updates & build pics coming! It warms my heart to see the very first generation YZF getting a rebuild and some long deserved TLC! 
Cheers! 😎 👍❗️

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Perky
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4/7/2026 9:34pm Edited Date/Time 4/7/2026 9:35pm
Hey Perky! I hope your build goes really well and you get the bike restored in a way that will make all your wildest dreams come true...
IMG 9598 3.jpeg?VersionId=RaY8Cz2ML9mK9aWldLYDzXzz7XkWf7GIMG 0848 1IMG 9602 3

Hey Perky! 
I hope your build goes really well and you get the bike restored in a way that will make all your wildest dreams come true! 🤪

My brother and I had em and we LOVED them! I had a 98 & 99 400, a 2000 & two 2002 426’s and they were all fun/fast bikes, once you got the feel for the thumper and came to terms with the compression braking! 
(First pic is my brother & I, amateur Sunday, AMA Arenacross @ Lazy E Arena, Guthrie Oklahoma. Second two are me, then my brother, on different jumps at our local track, the infamous Midwest track, Motorcycle Raceway in Oklahoma City! Known far and wide by MX’ers all around this part of the country as … 59th & Douglas! 😝)

One old trick I would pass along during the engine rebuild that you might consider? IF you’d care to avoid the starting drill that the compression lever was famous for, consider having the exhaust cam from the 2003 YZ450f  installed in the 1999 YZ400! The 2003 YZ450 cam with the auto-decompression built into the cam, is a direct / drop-in replacement and will eliminate the ridiculous starting drill, as well as avoiding having the compression lever on the bar! (And the associated damage that could result from unintentional engagement!)

Keep the updates & build pics coming! It warms my heart to see the very first generation YZF getting a rebuild and some long deserved TLC! 
Cheers! 😎 👍❗️

Thanks for the post! I actually haven’t heard of the auto-decompression trick, but I messaged the engine builder and we’ll see if they’re able to add that in. 😎

Edit: Did you guys make the vented number plates yourselves or was that something you could get off the shelf back then?

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BoxcarWilly
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4/7/2026 9:46pm
Perky wrote:
Thanks for the post! I actually haven’t heard of the auto-decompression trick, but I messaged the engine builder and we’ll see if they’re able to add...

Thanks for the post! I actually haven’t heard of the auto-decompression trick, but I messaged the engine builder and we’ll see if they’re able to add that in. 😎

Edit: Did you guys make the vented number plates yourselves or was that something you could get off the shelf back then?

Acerbis made half vented front plates. They were relatively common back then so you should be able to find one. I have several, but they’re the 96-98 front mount style instead of the 98+ top mount.

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motorick5052
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4/8/2026 7:59am Edited Date/Time 4/8/2026 8:04am
Perky wrote:
Thanks for the post! I actually haven’t heard of the auto-decompression trick, but I messaged the engine builder and we’ll see if they’re able to add...

Thanks for the post! I actually haven’t heard of the auto-decompression trick, but I messaged the engine builder and we’ll see if they’re able to add that in. 😎

Edit: Did you guys make the vented number plates yourselves or was that something you could get off the shelf back then?

What Willy Said! 🤪

The vented plate was the ACERBIS model that was readily available at the time! It was from the era when number plates were still designed to ACTUALLY display numbers that could be read as the bike passed by! 😝 

When Yamaha released the 2003 YZ450F with the decompression built into the exhaust side cam (eliminating the manual lever & cable system of the 400/426, as well as the potential damage that could result from the lever being activated in crash etc!) it instantly made ALL the earlier generations feel wildly antiquated! Many guys with brand new 2002 426’s (which by the way, was identical to the 400 w/a small change to bore!) suddenly had a very dated machine and it did NOT take long before someone (way smarter than me! 😊) determined that the 2003 exhaust cam was a direct/drop-in replacement and their was a mad rush to acquire/install the 03 exhaust cam in the previous 400/426 models! 
A local Yamaha shop in Oklahoma City at that time (closed now!) Baker Boys Yamaha, was very active in the moto-scene, (owned by Chan Baker, a fast A rider in his day! His son Chandler Baker, is currently racing professionally!) and the shop sponsored a number of midwest fast guys… they were installing HOT-Cams into the brand new race bikes before they were even ridden! This left MANY brand new stock Yamaha cams lying on the shop shelf! I got ahold of two of those “used” but straight out a brand new 450 from Baker Boys and installed them in my & my brother’s bikes and it instantly made the 400/426 feel like the more modern 450, as the insane “kick through to TDC, activate manual, roll just passed TDC, release manual, kick, repeat” starting drill became a thing of the past!  
The 03 450 exhaust cam was FAR & AWAY the best modification we EVER made to those bikes! ‼️

Word eventually got around at my local MX track (59th & Douglas! 🤣) and over the next two years or so, I made a NICE little profit from other 400/426 guys approaching me at the track, asking “Are you the guy that can/will install the 450 cam in my bike” 🤔?! 
I’d have them acquire the 450 cam, bring me the bike clean with seat, tank & radiator shrouds removed after work one day, install the cam that night & pickup the bike ready to go next day! I was charging HALF what the shops were charging & still making $$$ as I had NO shop overhead etc, and the owner was getting his bike updated without paying shop labor rates SO everyone was happy! Even the shop was happy because they were selling all those brand new “used” cams for a good price too! 🤪

Those were fun magical times! I still ride & love moto even now…but the 1980/90/early 2000’s when my son got old enough to start riding/racing with me will always be the golden days of Moto for me! 
Good luck with your restoration! I really DO hope yer engine guy can drop-in an 03 exhaust cam for you! It’ll make that venerable ol’ 99 much more fun & NOT feel so old dealing with that ancient starting technique! 🥵

Keep us posted on your progress! 😎 👍❗️

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motorick5052
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4/8/2026 3:26pm Edited Date/Time 4/8/2026 3:29pm

( 😗 pppppppfffffffftttttttttt!!!? Hey thumbs-down Guy …. Over here …  🖕❗️🖕 🤬 🫵❗️)

Scrolling through this entire thread, nearly EVERY post has ONE thumbs down, and there is NO doubt they’re likely all from you, the same miserable POS, with nothing better to do than sit there pissed off that all the porn sites kicked you out after declining your credit card BUT do us all a favor and start practicing what your Mother & Grandmother probably told you MANY times in your wasted youth…   
“Remember, IF you don’t have anything nice to say, just don’t say anything at all!” 

IF you have NOTHING of value to add to a few guys chatting about a restoration project on a cool old MX BIKE on an MX BIKE FORUM then feel free to just scroll right on by…and while your at it, feel free to cram your thumbs down straight in your cram-hole on the way out the door too loser! 🖕 🤬❗️

 

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motorick5052
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4/8/2026 8:24pm
IMG 0859 3.jpeg?VersionId=o73OaDzjhAu39oaYL5qehBzUq

While looking at your pics, I couldn’t help but notice your project has an aftermarket upper clamp, and from memory it LOOKS like it might be an APPLIED Racing upper clamp? 
Whats left of that front numberplate appears to be the 1998 style plate, with the bolt going horizontally THROUGH the front of the plate and into the clamp. In 1999 Yamaha redesigned the plastic with the bolt going behind the plate vertically through a plastic tab and down into the top of the clamp. 
If memory serves me correctly, the APPLIED Clamp came with a machined tab that could be used with EITHER the 1998 style w/bolt through number plate OR 1999 style w/bolt behind number plate. 
Based on what it appears you currently have there, IF you can get your hands on the 1998 style ACERBIS stadium plate (like in my pics!) it would bolt right up to your current clamp! (If that helps any!?) 

What’s the word on that subframe in the pics? It does NOT appear to be the OEM subframe from the 1998/99 YZ that I remember? From memory both years had the subframe painted the same color blue as the frame… 

The subframe on your bike is curious / interesting in the pics too? 
Good luck w/your project! Will be anxious for updates when you have them! 😎 👍❗️

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450exc115
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4/9/2026 5:07am Edited Date/Time 4/9/2026 5:10am
While looking at your pics, I couldn’t help but notice your project has an aftermarket upper clamp, and from memory it LOOKS like it might be...
IMG 0859 3.jpeg?VersionId=o73OaDzjhAu39oaYL5qehBzUq

While looking at your pics, I couldn’t help but notice your project has an aftermarket upper clamp, and from memory it LOOKS like it might be an APPLIED Racing upper clamp? 
Whats left of that front numberplate appears to be the 1998 style plate, with the bolt going horizontally THROUGH the front of the plate and into the clamp. In 1999 Yamaha redesigned the plastic with the bolt going behind the plate vertically through a plastic tab and down into the top of the clamp. 
If memory serves me correctly, the APPLIED Clamp came with a machined tab that could be used with EITHER the 1998 style w/bolt through number plate OR 1999 style w/bolt behind number plate. 
Based on what it appears you currently have there, IF you can get your hands on the 1998 style ACERBIS stadium plate (like in my pics!) it would bolt right up to your current clamp! (If that helps any!?) 

What’s the word on that subframe in the pics? It does NOT appear to be the OEM subframe from the 1998/99 YZ that I remember? From memory both years had the subframe painted the same color blue as the frame… 

The subframe on your bike is curious / interesting in the pics too? 
Good luck w/your project! Will be anxious for updates when you have them! 😎 👍❗️

Definitely an applied clamp, I had them on my 98 YZ250.  Looks like an AC alum subframe.  Stock were blue painted steel till 00 and then the newer factory alum ones were made of square stock.  What's crazy is that Yamaha sold a Titanium one through their GTY catalog for $150 back in the day. I wish I had picked one of those up as now they are nearly impossible to find. 

I wrote a college paper on the YZ400 and the high performance 4-stokes that took over the racing in the early 00s for a grad class.  I think I still have the magazines for the 97 YZM400 and then production YZ400.  I bought my first new bike in 98 a YZ250 as the 400 was near impossible to find.  I got my first out of college job in March and had the YZ250 in April, by then the 400s were gone.  Yamaha was running their 0, 0, 0 financing.  zero down, zero payments and zero interest for the first 6 months.  Good times.  Still have the bike even..  Probably time to start building it.  

98 YZ250 HS Racing
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Perky
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4/9/2026 7:59pm
While looking at your pics, I couldn’t help but notice your project has an aftermarket upper clamp, and from memory it LOOKS like it might be...
IMG 0859 3.jpeg?VersionId=o73OaDzjhAu39oaYL5qehBzUq

While looking at your pics, I couldn’t help but notice your project has an aftermarket upper clamp, and from memory it LOOKS like it might be an APPLIED Racing upper clamp? 
Whats left of that front numberplate appears to be the 1998 style plate, with the bolt going horizontally THROUGH the front of the plate and into the clamp. In 1999 Yamaha redesigned the plastic with the bolt going behind the plate vertically through a plastic tab and down into the top of the clamp. 
If memory serves me correctly, the APPLIED Clamp came with a machined tab that could be used with EITHER the 1998 style w/bolt through number plate OR 1999 style w/bolt behind number plate. 
Based on what it appears you currently have there, IF you can get your hands on the 1998 style ACERBIS stadium plate (like in my pics!) it would bolt right up to your current clamp! (If that helps any!?) 

What’s the word on that subframe in the pics? It does NOT appear to be the OEM subframe from the 1998/99 YZ that I remember? From memory both years had the subframe painted the same color blue as the frame… 

The subframe on your bike is curious / interesting in the pics too? 
Good luck w/your project! Will be anxious for updates when you have them! 😎 👍❗️

Sharp eye! It is in fact an Applied clamp. I wouldn’t haven’t known it was much different than OEM had you not shared about the mounting points on the Acerbis number plate.

On the subframe - hard telling. The previous owner cracked it at the lower right mounting tab, so I’ve already dispatched what was on it for another ‘99 OEM subframe I sourced awhile back from eBay. I’ll post pics soon.

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motorick5052
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4/10/2026 3:14pm

Thats great to hear you have an OEM subframe to  replace whatever that mess was that was on in the first pic! It appeared to have really poor fit & finish around the airbox etc! The OEM will assure a nice factory appearance when its all done! 

😎 👍❗️

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Perky
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4/14/2026 9:48am Edited Date/Time 4/14/2026 9:48am

Received some photos from my engine guy… no bueno. However, he did get my last minute request to change out the exhaust cam to the auto decompression style! Excited to have it repaired and returned in another 4-6 weeks. 

IMG 2117 4
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motorick5052
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4/14/2026 7:03pm Edited Date/Time 4/14/2026 7:04pm

🥵 That is  U G L Y! 
Does your engine builder think that cylinder is salvageable, or gonna have to replace that? 
Either way I hope there’s a quick/affordable solution and it’s back together without too much issue!

What is your plan for a replacement fuel tank? I noticed the tank was in as a good condition as the front fender! 🤪 

Were you planning to restore it to Moto or off road use? I’m sure ACERBIS probably still makes the off-road oversized tank for it, but if you’re interested in OEM size/style, I have had EXCELLENT luck with CLARKE MFG stuff! 
If memory serves me correctly, the ONLY piece from the 98 that is different is the front plate, as we have discussed! Yamaha restyled the front fender, but the 98-2002 will bolt right up! All other plastic will interchange between those first five years! 
Hopefully there is still NEW replacement plastic available to you for the ol’ YZ400/426F!

Looking forward to seeing it aback together! 😎 👍❗️

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Banana_oil
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4/14/2026 9:44pm

The shrouds are actually different on 00-02 as the fixation in the radiator is angled.

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Perky
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4/16/2026 4:57am
🥵 That is  U G L Y! Does your engine builder think that cylinder is salvageable, or gonna have to replace that? Either way I hope there’s a...

🥵 That is  U G L Y! 
Does your engine builder think that cylinder is salvageable, or gonna have to replace that? 
Either way I hope there’s a quick/affordable solution and it’s back together without too much issue!

What is your plan for a replacement fuel tank? I noticed the tank was in as a good condition as the front fender! 🤪 

Were you planning to restore it to Moto or off road use? I’m sure ACERBIS probably still makes the off-road oversized tank for it, but if you’re interested in OEM size/style, I have had EXCELLENT luck with CLARKE MFG stuff! 
If memory serves me correctly, the ONLY piece from the 98 that is different is the front plate, as we have discussed! Yamaha restyled the front fender, but the 98-2002 will bolt right up! All other plastic will interchange between those first five years! 
Hopefully there is still NEW replacement plastic available to you for the ol’ YZ400/426F!

Looking forward to seeing it aback together! 😎 👍❗️

$295 was his fee to repair the cylinder, Clarke still makes an OEM replacement for around $260, and while I couldn’t find it on Acerbis website, I did snag a NOS Acerbis full replacement plastics kit on eBay a couple months back. Also received the the replacement seat and airbox this week, so as soon as the engine is back she’ll look much, much better.


I’ve already got a ‘05 RM125 and a ‘04 CR250 for my moto bikes. Lately I’ve been on the hunt for a cush drive hub and a set of 17” rims to build it as a supermoto for track use. The two road courses in New Mexico are both pretty rough, and very short, so if done right my 25+ year old bike should not only look cool but occasionally whip up on some R3s and R6s.

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