We're similar except that I have a full exhaust. Check eBay for a replacement can. That stocker, even drilled, just chokes the bike. The midpipe that connects to it isn't much better.
I'm running a 135 main with the full exhaust so your 125 main MAY be a little lean. If the bike takes full throttle when warm but in cold weather, you're likely OK.
Your hesitation is the classic Suzuki EPA-approved condition of the Bandit 1200. Lean at the test RPM. If you've never played with the needles, raise them one shim and it will go away. A washer kit is available at Radio Shack (it's in the drawers). Put a bunch on a wire or screwdriver to pick 4 that are closest to the same thickness. If you need 2, go ahead. Just remember that one shim too many can cost 10 MPG. Some have needles that have adjustable clip positions so moving the clip down the needle one position will be about the same as adding two shims.
Make one change at a time and put a good 50 miles on it between changes for a proper eval. Good luck!
Marc/Atlanta
'99 B12
2" mod, Holeshot exhaust, K&N, 135 main, 35 pilot, Dale needles