2000 Gt to 96 cobra questions?

I'm not sure if you could wire the COP system to use coil packs; I know it's possible the other way around (still in a waste spark config). You could get valve covers from a COP 4V and run COPs though (if I recall correctly the polarity is reversed on a 4V COP). The 2V ECU should be able to run it otherwise.

+1 on above.

IMO the only way this swap works is to use the original 2000 GT wiring harness WITH COP's. It's not possible for a PCM from a 2000 to run a coil pack ignition system. Why? Think about it. For a coil pack system using a waste spark system, there are (4) coil drivers. Where as a COP ignition system uses (8) ignition coil drivers.

the 2000 ecu can be setup to run coil packs no problem. Ive tuned several hundred of them and never once had any problems.

your only going to use 4 outputs

ecu pin#s
pin 26 coils a and e
pin 52 coils b and f
pin 78 coils c and g
pin 204 coil d and h

coils fire a-b-c-d-e-f-g-h
cyl fire 1-3-7-2-6-5-4-8

a=cyl 1 and e=cyl 6
b=cyl 3 and f=cyl 5
c=cyl 7 and g = cyl 4
d=cyl 2 and h = cyl 8

you can see its the same firing order as cdan4 which is the early 1996 eec-v
http://www.efidynotuning.com/pinouts.htm

its a simple switch in the tune to control it correctly

but as has been stated the 4v COPs are preferred.