When I did this. I used a 302 from an 85 Grand Marquis, a C-4 from a 76 Elite, and a Motorcraft 2 barrel carb. I just yanked the CFI crap off and slapped on the carb. The motor mounts are the biggest issue. For some reason, the 87-88 Birds used different motor mounts than any other Ford. You might consider an aftermarket K-frame. That would eliminate that problem. I also used a cheapo electric fuel pump.
Kywookie just put a 351W in a 87-88 Cougar and might have more information. TurboCoupe50 also has swapped a turbo 4 for a 5.0 so he will have lots of info. Mine is in a circle track car so I didn't have to worry about streetability. Hope this helps. If you are wanting to stay with EFI you will need all the 5.0 electronics. They are completely different for the 3.8, I think.
Here's a pic.

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