OK, I'm officially giving in and allowing my p'up to do anything it want's as long as it keeps going. After running through the injection cleaner and a couple fresh tanks of gas the roughness has smoothed out, dying on a cold start has stopped and I've picked up another half mile per gallon, but I still can't get the rpm's up and it still has the hesitation on acceleration. I'm pretty convinced it's the throttle position switch, mostly 'cause that's the only thing left that would explain the symptoms.
Being that it's a $90 item at the local dealer I'll put up with less than perfect performance until something more definite tells me I have to replace it. Thanks for the tips and feedback.