2006 YZ450f backfire!

The popping in the exhaust is a sign of a lean condition. There are several causes. One is the fuel screw setting under the carb. A bit hard to get to, but CCW rotation richens the fuel mix. CW leans it out. 1/8 of a turn make a big difference.
If that does not cure it after about 1/2 turn, then I would be looking at the exhaust pipe gasket at the head. If the pipe has ever been removed it will need to be replaced as they are a crush gasket intended for a one time use.
The last item would be a partial clogged pilot jet in the carb. If that is not clogged, the exhaust gasket was replaced and the fuel screw adjustment did not fix the issue, then you may need to go up one size on the pilot jet.
Also, have you checked the valve clearances and cam timing?

Paw Paw

Another item that commonly causes a lean condition is the hot-start hanging open. Where the plunger fits in the carb it gets gunked up and sticky. Take it apart, clean everything well and put a light coat of grease on it. Then make sure the cable is nice and free and the finger lever has a little bit of play in it so it's not keeping tension on the cable.

my first thought would be that your valves are too tight which could lead to the popping and some hard starting issues, but it sounds like you have done all that, so id move on to the carb and work with the jetting like paw-paw suggested. there are a lot of youtube videos on carb tuning to get you started.

There are also some tricks you can do with the carb that in my opinion are worthwhile doing. one being the accelerator pump mod that will give you some more fuel down of the bottom and really clean her up down there.

the second gets that useless raccoon pecker yamaha calls a "hot start lever" off the bars. essentially wire that thing closed, use an oem yzf450 quad hot start block off plate and it gets rid of the hotstart.

if you google both of those, your answers will be right in front of you in google images

I have the same model year bike. As stated above its mostly likely your fuel screw. It's worth while buying the aftermarket style that lets you adjust it with your fingers as major elevation/temperature changes will cause it to lean out enough to pop on decel. If that's not it then work out the correct jetting.

Too lean on the pilot could cause this. At your elevation a 45 or 48 should be fine. I see the o ring on the fuel screws damaged a lot of the time and this will cause it as well. Another less likely thing I have seen is varnish in the nozzle (the part the needle goes in and out of), this will cause a big or backfire as well.