If you're looking into an automatic, make sure it shifts smooth on all upshifts and during torque converter lockup. If it seems harsh, steer clear from that particular truck because it'll eventually fail. My 05 was brand new and it had a pretty poor automatic transmission, but it started around 8-10k miles and failed at 21k. When the back wheels hop on a 1-2 upshift, you know you've got a bad trans. Pay close attention to the 4-5 upshift and 5th gear lockup too. If it shudders when it locks up, it wasn't taken care of.
If you're set on a manual, I can't help you there.
A lot of the guys with the TRD S/C seem to get pretty good MPG with it as long as they keep from flooring it everywhere and destroying their tires.
It has a bypass valve that recirculates the excess boost back into the S/C, so you won't get any boost surge on upshifts or deceleration. The S/C's power gains are underrated since Toyota heat soaked the intercooler during SAE testing to reflect real world driving. I'd get one if I had the funds.