I'm not sure how much this helps....
It does sound like someone hacked the harness. To my mind, the harness should have been converted bumper to bumper. Anything else is a bodge that is bound to have problems.
If you are having problems, the MF that installed it is the one that has to fix it. If they don't or won't then sue them in Small Claims Court. (SC court is an amazing invention.)
That said....
87 is the "best" of all Fiero years. It fixes the vast majority of things without the increasingly limited availability of 88 suspension parts. (Never buy any car that is available only one year unless you have money to burn or love headaches.)
I would happily convert any 84 to the 87 harness but only if it can be done bumper to bumper. That includes the Gen 2 Headlight Motor system. The dificulty here could be the engine. I don't know if the 84-86 distributor based L4 can plug into the 87 car harness. (Even if you change an 84 engine harness to a 85-6)
It would be nice if the Fiero all had the same harness but there are actually several. There are enough things differant between them that older year stuff might not be plug and play.
The total sure solution would be to change the 84 to the 87 harness AND the Gen 2 HL motors AND change to an 87/88 DIS L4. This would fix a whole bunch of issues.
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11-Sept-01, The day the world as we knew it ended.