Whatever the case there is a way to make the hookup. If you have access to junk cars, get a junk dash-end from the '99 with a few inches of wire. Get a pigtail for installing a new stereo in the '88 or cut the radio-end connector off any standard harness adapter for installing a new radio in an '88. Then you'll have an '88 radio-end connector with a few inches of wire that will plug into your dash. You'll have a '99 dash-end connector with a few inches of wire that will plug into your new radio. So, if you connect the right wires together you can just plug everything in and go.
You will have certain wires that almost certainly are the same. You will have +12V (main power, on with accessories), ground, light (+12V with parking lights on), memory (+12V always on), front left speaker + and -, front right speaker + and -, right rear speaker + and -, left rear speaker + and -. As long as you have a reference for what wire does what on each unit you can hook them up right. These should be all you need to get it running and for it to work with the '88.
Aron