Jordan,
I just did a complete build of my engine and I was experiencing the same issue... car just didn't feel strong like I expected for the mods. I was throwing a code 51 occasionally and someone gave me great advice to get that taken care of before I tried anything else... so I adjusted the TPS back to proper specs, cleared the codes and went for a short drive... felt MUCH better but still not quite where I expected it to be... so I decided to check the timing... I had just checked the timing earlier today and it was at 10.5*... well after adjusting the TPS it was now at 0*. So I retimed it and put it back to 10.5* and obviously the idle smoothed and when I went for another drive it was exactly what I was expecting from the car.
So if you have a bad tps, misadjusted tps and stop screw or anything at all wrong with any of these... I would fix that before you worry about anything else... get the stop screw handled and then adjust your tps to spec using an ohm meter and thickness guage. The tps may not be bad but just not adjusted correctly... I thought the same thing at first.
If the bad tps is causing the car to retard the timing you will experience most of the issues you have been describing.
Good luck!