We've done a couple of Series 3 swaps but always used the N* throttle body that is cable operated. This required using the 2003 PCM to shift the tranny. No earlier PCM will shift the 03-up transmissions. So in essence we used Series II control.
As Charlie said you could do a full series three swap using the accelerator pedal module and keep the electric throttle body but some serious reprogramming of the PCM might be required. The later 3800 systems were used in conjunction with traction control and I believe wheel sensors. I don't know if that's the best route to performance but a good programmer should be able to help you with a work around. Good luck on the swap, you'll love it.
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" THE BLACK PARALYZER" -87GT 3800SC Series III engine, custom ZZP /Frozen Boost Intercooler setup, 3.4" Pulley, Northstar TB, LS1 MAF, 3" Spintech/Hedman Exhaust, P-log Manifold, Autolite 104's, MSD wires, Custom CAI, 4T65eHD w. custom axles, Champion Radiator, S10 Brake Booster, HP Tuners VCM Suite.
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87GT - ALL OUT 3.4L Turbocharged engine, Garrett Hybrid Turbo, MSD ign., modified TH125H
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