Nate:

A couple of things here strike me as odd... They might give some insight as to why you're misfiring...

-Wires: Wires will cause misfires very quickly- Are they brand new? Worn in any way? Did you use dielectic grease between the wires & plugs, and wires & coil?

-Copper plugs: The SVT cams and computer that you're using are computing A/F and timing based on a very hot, platinum-based spark. The only time I've seen coppers is under FI.

-Rich condition: Unburnt fuel and carbon build-up from those misfires. I would tend in this case to verify the MAF/Injector combo. Which injectors are you using? Are you positive on the MAF calibration? Extreme rich in the low band is screaming either bad induction or bad A/F calculations.

-TPS: After installing the new TPS- Are you properly calibrated? Proper voltage ratings are critical at closed and WOT. This would throw off the A/F mix really quickly.

-MIL Eliminators: Recommend these, but only to avoid the "catalyst below efficiency threshold" CEL. Those two O2s are for that function only- I have seen no evidence that their signals influence A/F mixture.

Hope something here turns on a light for ya...

Dan G. and his Cougar Forged internal (Diamond & Pauter) full 3L, "Monster" Kinger F/I cut & P&P, T3/4 60 trim .82A/R ADC turbo, SPEC Stage 3, Torsen, Greddy Profec-B SPEC II, Apex'i Timer, Lots of Gauges! Used to have: 3.0L SVT hybrid