Not to rain on your parade, but how much power do you expect from the power commander? To paraphrase the old hot rodders, "There's nothing like cubic centimeters". To get more low-end torque, you need a big-bore kit.
You could get a GSXR 1000 engine (there must be lots of wrecked ones), but the 1000 engine's bore is only 1mm larger than yours. The 1000 gets it's extra cc's from a 13mm longer stroke. Lots of torque with the stroke, but it doesn't match your revs. I would compare the costs of getting an 1000 engine, with cylinder boring and new pistons.