I did the swap for my 88 GT with a 3G too. So why not with your 86.
I used these HOW TO to help me in my project.
AMP Alternator Upgrade
Amp Alternator Project
AMP 3G "small Case" Alternator
Anyway i installed a Mach 460 sound system from a 2000 stang in my 88 without any problem.
Stangs are easy to work on.