i just bought a 98 cbr 600 f3 it came with no motor and a two brothers racing full exhaust, i installed a new motor and exhaust also put in a dyno jet kit in with a k&n filter. i used 38 main jets in the outer 2 carbs and 40 main jets in the inner carbs like the manual says. my problem is after i got everything put together it runs and pulls hard in 1st gear and then in second kind of bogs down in high rpm and 3rd gear it loses all power and wont go any faster. When i take the air box lid off it runs a little slower in 1st gear but it runs good through 6th gear. how can i get it to run good through all gears with the airbox lid on

 

this is a complete guess as i have no experience with anything like this. check for anything broken in the ram air tubes. it seems to me if there was a broken piece of plastic in there, the faster you go (getting into higher gears) the wind could push the broken piece back blocking air from getting into the sealed air box. first gear wouldn't have enough air pressure in the tubes to force the broken piece up so it works properly. when you take the air box lid off, it doesn't work as efficiently as it would using the ram air tubes but because the air isn't as restricted as it was using the air tubes in the upper gears they seem to work better.