How much are you swapping? Just the block and head?
There was a big change in the intake in '89, and '88 got the Air Suction system (big reed valve and plastic resonator thingy under the intake). You're better off just putting the '86 intake onto the later head. Everything else should bolt up.
There is an advantage to installing the upper half of the later plenum, there are several write-ups on this, I'm in the middle of working thru this myself. Throttle body is a little better. You also get rid of that air valve thing. Supposed to be better throttle response.