I've got an all stock 87 T-brid 3.8 CFI last year I put new timing chain on it and rebuilt the CFI unit. The car runs much better now. Recently My son Purchased a 03 mustang 3.8 that needs a new engine. We are in the process of an engine swap. I will have a complete 03 3.8 to play with. Currently it runs but has a very bad shake to it and has broken a piece of the oil pan. I wonder if the heads from the 03 would bolt onto the 8.7 bottom end so I could use the newer style EFi setup. Yes I know I would need the harness and ECU to make it run. Just thinking of a way to get more power in the 87 3.8 with parts I will have on hand.
I've been doing a lot of research and found some good information on the differences in the 3.8's Here is a link: https://www.enginebuildermag.com/2001/09/rebuilding-the-ford-3-8l-engine/ I do find that while the heads might bolt on the old block there are enough differences that I beileve the only way would be to use the newer style block that is setup for the balance shaft and the roller cam shaft. That being said I'll just have to hunt down a good bottom end. I have purchased a complete harness and Ecu from an 03 mustang 3.8l. I do wonder if this will work with the 87 trans?
The automatic in our cars is 100% mechanical as far as control goes. There is a linkage setup from the throttle body down to the transmission. With that said, there would be no way for EEC controls to be implemented. That's not to say that you couldn't make a way to convert your transmission to use a TV cable, and interface the throttle body so your transmission can work like it should.
There are other options, such as maybe converting your car to manual using the transmission from a 94-04 3.8L, or converting it to the automatic that came with the same generation (AODE?). None of it is impossible, but with that much work, you would probably be happier with a different swap.