this thing i driving me crazy!!!!! i have a gixxer 1k but a friend is having a problem with his 99 busa so i say bring it over i ll take a look.i will start from the beginning.he comes over i take it for a 15 mile thrashing... it ran great!!! he told me to keep it for a couple of days "you will see" he says. well i left it in the driveway for about 45 min. then i take out again it seems like its not getting enough fuel spitting and sputtering like you took out 3 plugs and tried to ride it. wont idle wont rev it acts like its got a 4000 rev limiter.i unhooked the powercommander and got the same result. i left it until the next day went out rode it for 40 miles ran great again!! stopped for a little 30 minute break got back on and here we go again spitting and sputtering!!! the tank was painted not long ago so i pull the petcock to check out the screen. it seemed to be clean but i got some settlement out of the tank...hmmmm maybe it was clogging the screen. i cleaned everything out real good and put it back together. everthing still acts the same no change. i took apart the fuel pump and checked the filter...everything was very clean.
i called the dealer the said it was the tip over switch so.... i ripped it apart..everthing was working just fine.

what i am getting at is ......has anyone had a simalar problem...if so drop me a responce.i will keep everone updated!!! thanks foir any help.

the gas line could be crimped when you let the tank down i had the same problem with my busa. sometime it would not rev over 5 grand it just got stuck there like it had no more. i bet its the gas line

could be>

Kinked fuel line
Clogged fuel pump filters..there a few of them in the pump are You sure You got them all??
Try changing the plugs too??

The 99's are know for fuel filters getting clogged..