Rock/Jock- Once again, note that you have a SECOND Gen. Bandit... so a lot of the carb settings aren't the same as 1st Gen.
(for you F.I. guys... yer on your own!)
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Here's a little bit of "Jetting 101" theory, for anyone out there maybe without tons of jetting experience, (and please, anyone is welcome to correct me! I'm certainly not an "A" mechanic!)
Mid-range problems: remember, we're not usually talking about RPM levels as much as THROTTLE position. A 3000 rpm stumble while "cruising" isn't necessarily the same problem as a power-curve "flat-spot" when nailing the throttle wide open. You'll have to try and identify out when and where the "problem" comes on.
Basic throttle openings vs. fuel circuits-
1. WIDE OPEN :Mains
2. HALF-OPEN PLUS : Mains and needles
3. CRUISE :Mostly needles, some mains, some pilots
4. OFF-IDLE :mostly needles and pilots, influenced somewhat by fuel screws
5. IDLE :Pilots and fuel screws
Each overlaps the other to a different degree.
Jetting is such a pain in the azz (for me)... always has been... but it's SO WORTH IT when you finally get it sorted out properly and the bike is suddenly CRISP across the total rev range, with no flat spots. (And after all, isn't that so much more desireable than just saying "IT'S FASTER NOW"?)
Unfortunately, unless you're lucky, it usually takes a lot of trial and error to get it really sweet. (PS.. it may be a good idea to buy extra intake / airbox clamps because you may wear-out the screw heads after a while, if you're doing a lot of repeated carb-removal. The rubber intake boots might also eventually get stretched or cracked).
Investigating:
Start at the Top with your best-guess main jet size. Warm the bike up really good, and on a SAFELY deserted stretch of open road, whack it WFO wide-f&*$ing-open for 2-3 gears. Assuming it runs smoothly (no bogging or stumbling, hit the kill switch, coast to a stop, and check the plug color of a plug...looking for LIGHT TAN, of course. When that's good, work your way down to the needles, checking smoothness at mid-throttle openings and slow roll-on. Make adjustments if necessary... moving the little C-clip "UP" will cause a leaner condition; "DOWN" will mak it richer. Go lower to the pilots if necessary (but most pilots in my bikes haven't needed changing that I can remember). In the end, fine-tune the low-throttle openings with detailed fuel-screw adjustments (usually 1/4-turn increments at a time). Eventually, you'll get it. Just make sure other things aren't affecting your results, like dirty air-filters, mis-adjusted valves, or poorly-synched carbs.
TAKE NOTES on each change you make. You WILL forget, otherwise.
I had an Asia-only Honda 400SF in China, to which I added a carbon-fiber end can meant for a GSXR 750 (NEW condition, off EBay for only $80!), then chucked the clunky airbox in favor of individual Unipod filters. But no matter what I did after that, I COULDN'T get it to run. Barking, belching, spitting, stalling. Took me WEEKS and it was just driving me crazy, ran horribly and I was about to give up and go back to stock.. until some online-Aussie genius recommended a BIG jump in main-jet size. I ended going up a full, incredible FIFTY PERCENT larger on the main-jet sizes, and man, DID it EVER run!! That little F%*#er SCREAMED... probably picked up a whopping 15% power increase over stock. Suddenly, it was like a rat-monkey with it's ass on fire. I almost creamed myself when it finally howled to life cleanly. DAMN that thing would RIP across the Chinese farm roads. Loud and raspy as hell with that big, open D&D pipe... good thing the cops over there had no time for such details. PS..I did almost NOTHING to the bottom fuel circuitry; used stock needles and pilots... mostly just some fuel-screw tinkering.
Point is here, keep trying. Read all the stuff you can find on jetting...over-lapping fuel circuits, etc... how one affects the other... and ONLY MAKE ONE CHANGE AT A TIME, or you'll go nuts and never figure out what worked and what didn't.
Yes, it SUCKS to keep ripping that bank of carbs in and out, over and over... but you'll get better/faster at it, I asssure you.