exrider91: I'll look for the butterfly valve and try to test it.
I won't have access to the bike until this weekend. Thanks, for the tips. I'll post back when I get more info.

 

My 99 400ex is bored 40 over with a stage 2 hotcam. Recently it would bog down in 2nd gear under full throttle. Took carb apart and cleaned main and slow jet. Slow jet was crudded up a lil. Blew air and carb cleaner through it. Cleaned carb a lil with the cleaner too. Put back together and still didnt run right. Checked the spark plug for the hell of it and it was finger tight(very loose). Took it out fixed the gap to .025, cleaned with scotch brite pad and reinstalled. Now it runs like a beast again. Worth a shot on yours too.

 

I have a 2002 trx300ex and it seems like I have the same problem. I'm wondering if you found the solution

mine worked fine a few months ago until the battery died and wouldn't charge. after I put the new battery in, I turned the key on and the 15A fuse blew. so I put in a 20A and it blew, then i put a 25A in and it didn't blow that but the cdi started melting. after I took the cdi out, I put a 15A fuse in and turned the key and it was fine, so I guess my cdi had a short in it. I got a new cdi from fortnine.ca, put it in and it idles, but when I give it any amount of throttle it starts making the very aggressive whomp sounds and dies after a few seconds if I keep the throttle.

I've fully taken apart the carb and cleaned it times, used a new rebuild kit on it. when its at idle I sprayed a little quick start in through the carb and it immediately kills the engine, so I moved the needle down thinking its getting too much gas and it didn't change anything.

Everything is stock, removing the air filter and the exhaust changes nothing. it has a new spark plug, ignition coil, battery, rectifier, I bought a second cdi because i though the first one was faulty, turns out the second one is faulty causing no spark.
I hope I have given enough info to go off. any help is much appreciated