This is my first time adjusting valves after riding 2-strokes my whole life, and the Pro X valve shims only seem to come in .025 increments on RMATV/MC. This pushes me into possibly loose territory and unfortunately have nobody locally to really talk to about this. Do my calculations seem to be okay? I used a tool at Tokyo Mods to calculate the difference.

Going by what you have there, only that right exhaust is out and slightly out at that. You can shim that one and be good. I would get a complete shim kit instead of attempting to order the exact shims you need, it will make life easier. The intakes are close to spec but really no need to adjust them right now.
This gave me a particular amount of anxiety, so I really do appreciate the wisdom.
I'd rather be on the loose side than the tight side and would personally shim everything to be on the looser side while I was in there.
I second just buying the entire shim kit (make sure you order the right diameter shims for your bike) and being done with it.
You're erring more on the side of loose and so I have to ask as somebody new to the 4-stroke maintenance world, would that be safer than say a tighter nominal range like motoracer58 suggested, or is it just kind of personal preference? I would hope to make it through this year without doing another adjustment. (I only put about 20 hours a year on a bike generally).
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Generally, the clearance reduces, as the valve face/seat wear - hence the recommendation for “the loose side” of perfect. IE, they will tighten with wear. (Unlike most other things on the planet - including 2 stroke bore/piston clearance which you, and I are probably more familiar with.)
No real need to overthink it, if it is in spec then there is no issue. If the valves are in good shape and not wearing out currently then being on the tighter end will not make a difference. If you are purposely setting valves on the loose end in anticipation of wear then you already have any issue. It doesn't hurt to have them on either end of the spec, on the tighter side, yes they might wear out and be out of spec sooner.
The bad thing about being too tight is that it could get harder to start the engine, and have low rpm and idle issues.
The bad thing about being too loose is that the top end could become slightly noisy, but won't hurt anything unless they become really loose and you start to lose a small amount of power also.
Again, these are the extreme ends. If you are near the specs, you are probably good.
I didn't know a shim calculator like that was out there. I double checked the math against one I made. Checks out. I agree error to the looser side because they tighten up over time.
Also, for anyone going from a Yamaha to any other brand, friggin pay attention to intake vs exhaust side. I messed that up after switching.
Thanks guys, I really do appreciate it. Working on 2 stroke engines was definitely a less involved process for me my whole life, but that's okay, this is very useful knowledge to have. This bike is a 2016 KX250F with only 28 hours on it and knew the original owner. Always taken care of, but noticed it was taking more kicks to start over the last season. I'll take the advice and get things set up proper. I don't have anybody else to ride with out here, so getting input from everyone on the forum has just been extremely valuable to me.
I came from 2 strokes also and still ride them. Forced myself to learn 4 strokes when i had to. There are more moving parts, and you will soon learn that piston and rings arent as big of a deal as they were. They last twice as long as a 2 stroke. The bad part is, you have more electronics, fuel pump, valves, timing chain, tensioner, ect that can go bad. The more you learn about those, the better off you will be.
the flywheel is magnetic and that is at the bottom of that cavity, not really a big deal, just need to pull the ignition cover off like already said and it should be sitting down there.
Got it, thanks guys!
Just for added piece of mind for you, my son rides a 2017 KX250 and still haven’t had to adjust the valves. Granted he doesn’t ride very hard but valves are still in spec after 70+ hours. The newer 4 strokes require a lot less maintenance than what they used to.
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