The harnesses are different between automatic and manual.
The chips are different between automatic and manual. If you have the 88 manual ECM, use that one.
You really need a manual harness, but the quick and dirty way to get it running is to jumper the large purple and yellow wires on the transmission selector switch. That will allow the starter to work. You will also need to re-pin the big yellow wire in the "engine side" of C500 (next to the battery) to mate up with the big purple wire in the "car side" of C500.
Since the 4 speed does not have a reverse light switch, you will need to wire one up to the shifter. The 4 speed shifter has a reverse light switch as part of the assembly. You will need to run two wires to the reverse light wiring that was part of the automatic transmission connector.
Or you could swap in the Getrag 5 speed. Instead of running wires to the shifter, you would just connect them to the reverse light switch on the tranny.
The VSS (speed sensor) wires will also be too long.
If you have any other specific questions, I'll be happy to try to answer them. I don't have the time to do the work, however. Sorry.
Since the 88 ECM is looking for a 5th gear, it will always be turning on the shift light in 4th. You can either swap in an 86 4 speed chip (the 85 chip will NOT work in the later ECM) or just remove the shift light bulb.
There were a few other minor wiring issues, converting an automatic harness to manual, but nothing that is a show stopper.
Edit - Welcome to our obsession!