If you're converting a Formula, the tail light harness is plug and play, since the Formula and GT were the same, under the skin.
(I used an 88 GT harness, but earlier years may work, with the exception of the blower motor wiring. I don't know if that necessitated any other changes or not.)
86 and 87 cars may be a bit more trouble, but I'm not sure. 4 cylinder cars (including the 88) may be be even more trouble, since NO 4 cylinder car ever came equipped with a fastback body.
85s are a pain, since NO 85 came with a fastback. Several circuits need to be rewired. There is also the possibility of some physical interference at the rear corners of the roof, where the fastback clip wraps around the edges. (I have seen this firsthand with an 85 GT that was converted, although I don't know if it affects all 85s or not.)
84s? Anybody's guess.
Quarter windows are not an issue, IMHO. I have had Fiero Warehouse (aka Chris Cook) windows on my car for ten years. No problem whatsoever. They are still available. Several members of our club own them.
Tail lights are another issue altogether. But there are complete replacement tail panels available from PISA, and probably other vendors, still.
Edit - Would I do it again? I've thought about it. Probably not. It's kind of a "been there done that" thing.
I actually almost bought another car that was nearly identical to mine. A Formula with a fastback clip. Had a blown up 3.4, but otherwise was nearly spotless. Was "gunmetal" instead of "blue gray" like mine. I decided to go in a different direction and get a notchie instead.
Other than that, my only issue would be with the tail lights. And that can be gotten around. Sort of.