I honestly don't know about the auto tranny setup. Like you, I've understood that there isn't much ECU difference between the manual and auto tranny. The 88 diagram doesn't have any pin out differences. That's *not* true of later 22REs, but I'm not entirely sure when they switched computers.. I know they were different by 1993. You'd need to confirm your ECU pin out.

I assume you want to do EFI with the 22RE and keep your manual transmission?

Two ways to do it:
1) Pull the entire motor out, wiring harness and all. You could probably get it to run just as easily on the stock ECU without additional expense.

2) If you want to make it simple, pull the motor out. Keep your stock 1984 wiring and run megasquirt "fuel only" - which is simply an add-in harness for the EFI side of things. Keep the stock 22r mechanical igntion system. These wiring setups look like "painless" wiring. You can get them pre-labelled.

Basically my harness doesn't help here... If you get it running with my harness, you could have it running with the stock ECU.