01 Raptor dies in 3rd. gear

[the Z Man]

It runs great through 1st and 2nd, when you pin 3rd. its like it runs out of gas, wait about 10 seconds and it starts right up, you can run all day in 1 and 2 but seems to do this in 3rd..?
Have rebuilt the carbs and can't seem to find an issue, could it be the cdi or some other area not fuel related?
Bike has been bored and built, full exhaust and so on...

[HmF300ex]

The same thing happened to a friends 400, we got it out after we went duning together and it would run fine until we got it into 3rd gear, we rebuilt the whole top end, carb, checked electrical system and it still wouldn't get outta third. It ended up being the rubber flange that connects the carb to the air box. Guess the sand just dry rotted it thru. Check that, if not I have no idea what it could be if you checked everything, it may be the cdi but i don't know anything about the cdi, if the flange is not broken i would check out the top end since thats the next easiest fix, if its not that you could be losing compression but it shouldn't be running good in any gear if thats the problem.