Okay. I'm not an expert on the modular cars, but let's see what I can do since you asked.
The Lincoln Mark VIII came with the AOD-E transmission during it's production run from 1993-1998. During that time it was equipped with the 4.6L DOHC 32V engine, almost exactly the same as the Cobra's. I really doubt there are any differences between the Mark VIII block and the Cobra block, and I would be suprised if all the 4.6's didn't use the same bolt pattern on the transmissions.
If you were in a pinch for a computer, the Mark VIII computer should run the AOD-E, but I don't know if the Cobra's will since the Cobra was never offered with an auto tranny.
Basically, it doesn't seem like a real complicated swap to me on the surface. You shouldn't have to do any engine compartment mods, I would assume the tranny will bolt up fine, and you should have access to auto computers for the DOHC 4.6L from the Mark VIII.
As far as your other mods, I don't know how the rest of your systems will interact with the Cobra parts.
If I had more knowledge about the newer engines, I'd certainly share it.
Good luck,
Kell
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