I just finished modifying my 2008 WR450F by installing the GYTR AIS removal kit, the kit basically removes the AIS, cuts the gray wire, changes out the throttle stop with a shorter throttle stop (giving more twist of the grip), rejetting the bike with 175 main jet, 50 pilot jet, and 110 main air jet.
These are the jets that came with the kit, but it's a massive step up from the jets that come stock with the bike. I also installed an adjustable air mixture screw.

I also installed a FMF 4.1 exhaust system with a mega bomber header.

After installation of the above parts, I set the air mixture screw at 2 full turns out from being seated.

When I went to start the bike it seems like the compression has gone through the roof. It's very difficult to get started.

I got it started once before dark (I quit working on it tonight so as not to PO my neighbors), but the bike has become difficult to start and I'm not exactly sure what I can do from this point forward to make the bike start and run as dependable as it was running before the mods.

I did all this to maximize my power out of the bike, but now I'm concerned I did so at the expense of dependability in the engine.

Also, reviewing other posts it appears that the jets provided with the GYTR kit causes the bike to run to rich and increase fuel consumption massively.
I went with the jets in the GYTR kit with the idea that Yamaha knows more than I and this is the jetting I should run on the bike. I'm beginning to think this was a poor assumption.

I live at 500 feet above sea level and ride anywhere from sea level to 6000 feet above sea level.

Any suggestions would be greatly appreciated

I need help here too!!

I am in the same boat minus the air mixture screw and the pipe. Rode the last couple of days and could only get 48 miles to the tank with the mods stated above.

Put the stock pilot jet back in.
Fuel Screw/Pilot Jet
Fuel screw settings in the 'book' are recommended starting points. Every bike is different, as is the temp and altitude. Set the screw according to this method. Do it with the bike fully heated up.
Gently turn the screw all the way in. Now back it out two turns. Start the bike and fully warm it up, go for a 10 minute ride. Set the idle to speed to 1,500~1,800 RPM as best you can (I know, without a tach this is tough, just set it to were it idles relatively smoothly). Once warmed, slow the idle to the lowest possible speed.
*** When turning the fuel screw, keep an accurate 'count' of the amount you are turning it and record it in case you have to reset it for some reason. Makes life easier when you can just set it from notes Vs. going through the procedure again.***
Turn the screw in until the idle becomes rough or the bike stalls.
if it stalled, open the screw about 1/4 more turn. Restart it and slowly screw it in till you can just perceive a change.
If the screw can be turned all the way in and the bike still idles perfectly and does not stall, then you need to go down a size in pilot jet.
Now very slowly, open the fuel screw till the idle is smooth. Blip the throttle, let the bike return to an idle, wait say ten seconds. Confirm it is the same smooth idle.
If the screw has to be opened more than 3 turns to get a smooth idle, you need to go up a size in pilot jet.
If you find it does not stall with the larger jet but has to be open more than three turns with the smaller pilot jet, put the larger one in and set the fuel screw at 1/2 turn.
If the idle speed increased, adjust the idle speed knob to return the bike to a real slow idle speed. You must then re-visit the fuel screw. Keep doing this till the fuel screw is opened just enough to provide a nice steady idle at the lowest possible RPM. Once this is done, increase the idle speed to the normal one for your bike, typically about 1,800 rpm, but go by the spec in your manual.

Put the stock Main air jet back in, start with a 185 main. Starting with the recommended main, remove the airbox door and go for a ride (bike fully warmed up). Is it better or worse?
If it is better, you need a smaller main.
Go down one size, replace the airbox door, ride. Remove the airbox door and test again. Better or worse? If better, go down a size again. Keep repeating this till the test with the airbox door is worse.

If it was worse with the airbox door removed, tape over 1/3 of your airbox opening, test (airbox door on, of course).
If it is worse now with the tape and was worse with the airbox door off, your main is just right. You are done!

If it seems better, you need to go up a size in main jet. Then test it again (remove the tape). Replace the tape, test again. If with the tape on it is better, go up another size in main. Keep repeating this till having the tape on is worse than with it off.
To finish up and ensure you are set accurately, retest the bike with the tape off (airbox door on), ride it, then remove the airbox door (tape off, of course). Best performance should be with the airbox untapped, airbox door on.

Remember, the main only operates at WOT. Ideally, you want to be in 3rd or 4th gear doing the tests, hitting max revs (just shy of the limiter) for at least 10 seconds to get an accurate representation of the jet status.

Then test various clip positions.

Thanks William,
I'll give it a shot and report back to you.