My 3tj has been playing up for sometime now. i took the air filter out which was filthy and the bike ran absolutly fine. I brought a new standard filter from wemoto and as soon as i rode it again i had some major problems with flat spots and having to rev past 5000 revs for it to pull away with out stalling. Ive cleaned the carbs 3 or 4 times now trying to find the problem, thought the air filter had solved it but no. I really dont know where to go from here haha. If any one could help it would be very appriciated.
Cheers Tom

did you check that you have the correct jets etc. as if it ran better without it may have the bigger than needed with a filter?

Agreed - have you tried running the engine with the air filter in and fuel tank off.
If that works then something is obstructing the airbox.

There should be two short black hoses on a swivelling T piece fixed between each pair of carbs. Make sure they are not tucked up under the air box (i.e. pointing forwards toward the cylinder head) - if so rotate them through 90 degrees so they point away from the carbs (in the direction of the battery) This will ensure you get a clean supply of air into the float chambers which will aid low speed fuelling and may solve your problem.