I agree completely i have the same set up as you but have gone ahead and ordered a power commander and a cat bypass. not exactly sure how it will turn out. but once i have those in place i will have hit a wall. with no idea which direction to turn in. if all fails i will buy a rolling chassis and start from scratch on my own tinkering toy.
Please let us know what the results are from your planned mods, very interested to know how the power commander / cat bypass turns out. Are you getting it dynoed before and after? Could be some great info. Good luck .