The 91 harness won't work in the 88, by plug & go. Best best is to get an 89 harness or convert you 88 harness to mass air. The auto computer will work in a 5 speed car.
Just for reference, here's a list of all the compatible years:
89 harness should work for 86-89 as long as you're using mass air.
90 harness will only work in a 90. (B/c of air bags and dual dash connectors)
91 through early 92 harnesses should be compatible (single dash connector, fuel pump relay under driver's seat)
Late 92 through 93 harnesses should be compatible (single dash connector, fuel pump relay under the hood)
Computers from 89-92 are all the same. Look for the A9L sticker on the back cover for a 5 speed that matches your requirements. Example: E9ZF 12A650 AA" with the A9L code.