It really bites when you get a bike that has had a jet kit installed and the owner hasn't a clue as to what is in there. You need to start at the mains. Ignore the idle screws for now. If you've got pods, make sure they're clean and oiled properly.
Get it warm and up to about 5K in second gear and slam it. It should run all the way to redline with no hesitation. If it hesitates or seems to loose steam on the way up, too lean on the mains. Another good way of diagnosing lean on mains is to full throttle for 10 seconds and then let off to 1/2. If the bike lunges forward, you're lean.
I've varied my mains to two steps rich and, although power is a bit down, there were no ill effects. Best to check for lean.
Next, check your pilots. Stock 37.5s work OK but it's crisper with 35s. Bandits vary somewhat, though. At any rate, YOU need to know.
Next, if you've got that classic leaness near 4K or hesitation at part throttle cruise, raise the needles one shim at a time. Adjust the idle screws to best very low idle (so that the idle circuit only is in play) and then raise the idle to about 1200.
All this should get you running well. It's important to get the mains perfect. They affect most other circuits.
This is my experience and has worked well for me on my '99. YMMV.
Marc/Atlanta
2" mod
K&N
35 pilot
135 main
Holeshot needles