You aren't going to be able to go up 3 or more teeth on the rear sprocket and keep the stock chain. It will be too short. You can usually go up 1 or 2 though. You can get essentially the same gearing as going up 3 teeth in the rear by dropping a tooth up front and that will allow you to keep the stock length chain.
As for a cheap muffler, keep an eye out on eBay as well as the classifieds of this and other Bandit boards. Aftermarket B12 cans (any year) will work on the 600, too - as long as they come with a mid-pipe (ie; slip-on, not bolt-on). A B12 bolt-on can will work,too - if you have the matching B12 mid-pipe - and these are generation specific. Since the 600's muffler is welded to the mid-pipe, any kind of gutting will be difficult. If you're lucky enough to find the stuff, a Suzuki RF900's stock can with a 2000 or older (1G) B12 mid-pipe will give you more power and a healthier tone than the stock Bandit piece, but will not be quite as powerful as an aftermarket slip-on setup.