Your answers are here courtesy of Dale Walker.
http://www.holeshot.com/suzuki/bandit/650-1250/products/efi-supertune-pro/dynocharts
My experience, going from stock to Stage 1 to Stage 2 with only a slip on and stock headers is there are significant gains to be had. Typically low RPM power (torque) is more a product of engine design. You are not flowing as much air hence opening the intake and exhaust (and providing the fuel to match) doesn't show as much gain down low.
Honestly the 1250 has SO much torque right off idle it's just as well!
I would go Stage 2 with Dale's Super Tune Pro and a slip on. It is all the Chassis can handle, even with suspension upgrades. Wish I had just went Stage 2 from the start.
IMHO.....