The best head would be the one from a long stroke '89-'90 GSXR750R (not the more common standard GSXR750). These are also known as "Double R's" and/or Slingshot motors - named for the 40mm Mikuni Slingshot carbs they came with. Good luck. If you find one, expect to pay top dollar. It is highly unlikely one of these will be in the hands of someone who doesn't know what they have. Barring that, any longstroke (749cc) '85-'87 & '90 GSXR750 or '88-up GSX750F Katana will do. Use the GSXR cams with the head, but since the B6 has a different cam chain than the GSXR, you have to use the B6 cam chain sprockets on the GSXR camshafts. You can get more power with these cams in the stock B6 head, too.
As for headers, the stock ones work pretty good with the stock or rejetted 600 motor and a slip-on. You might get 1-2 more horsepower with a full aftermarket system. Most don't feel the extra expense is worth the small amount of gain. The weight savings isn't that big of a deal since the B6 isn't really light enough to do serious duty as any kind of racer.
You wouldn't run the GSXR manifolds unless you're running GSXR or other non-stock carbs that use the GSXR's spacing.
If you seriously want to get more power for your B6, the best bet is to just pull out the 600cc lump and swap in a 750 Katana or GSXR mill. The engines from a GSXR 1100 (1052 or 1127), GSX1100F Katana (1127) or B12 (1157) will also bolt in, but if you're gonna go for that, you'd probably be money ahead to just sell the 600 and buy a 1200. The price difference between a 1G B6 and a 1G B12 is very small these days. That way you get the power and better brakes & suspension... and if that's not enough for you, there's plenty that can be done to upgrade the B12 powerplant.
AFAIK, there's no aftermarket brain for the Bandit, but you can buy or make a timing advancer.