I believe the difference from 86-87 and 88-up, is the o2 sensor. It is a 1 wire in 86-87, and a 4 wire in 88-up. It will run the engine, but an o2 sensor code will occur.
I haven't researched it, but if you added wires / re-pin the harness, you may get it to work. The o2 sensor has a heater circuit on the 88 and up models.

Not sure why your efi fuse blew in the first place, but it may only be a matter of time before it blows again, especially since you say it stalled when wiggling the harness.

Or did you find the short while repairing your harness?

Keep update on if it blows the fuse again.