Rule #1 for swapping stuff with these trucks - match your main cab harness to your dash, and your door harnesses to your main cab harness.
In your case the '87 and the '89 dashes are near identical as far as electric stuff goes, there is some difference with the HVAC stuff but that's not related to what you're doing now. The door harness connectors should be the same between the 87 and the 89, meaning if you pull the harnesses out of your old 87 doors and stuff them into your new '95 doors they will work with your main cab harness and your 89 dash. Swap your 87 panel onto your 95 doors, it's a direct bolt-on job and gives you proper switches for windows and locks.
The reason you have extra connectors in the 95 doors is most likely for use with power mirrors, which wasn't an option back in 87. We actually added the power mirror harnesses into the factory door harnesses of both out pre-OBS Fords, neither truck is using them right now but if at some point in the future we decided we felt ambitious enough to tackle this project the wiring is already there...