i had my 88 motor in the original body but it got to rusty so i picked up a mint 87 body but the wirringharness does int match up ... what can i do to make this work for me ? thx

Steal the harness from the other body.

yeah, either that or use the intake system from the '87, if you still got it. 88's should start having the TBI, though, and that WOULD be more desirable.

There isn't a difference under the hood of an 87 and 88, I don't think 88.5 changed anything under the hood, either. Just some cosmetic things, 5th gear, and 1 rear brakeline.

Samurais didn't have TBI untill either 90 or 91, so if you have TBI, someone added it.

Some of the wiring harness connectors are different between the 86-88s and the 88.5-89s.....that is the difference he is running into.
As suggested, either swap the intakes on the engines or swap the engine part of the wiring harnesses, along with the tranny switches (since they will have different connectors on them too).
EFI wasn't added until 90.