Yes the tray that holds the ECU (ECM) is different. In fact, it's the same tray that's needed for the 7730 type that is used to upgrade the V6. Also, the 88 duke Fiero uses a V5 AC compressor, and is wired to work with that. If your 86 Fiero has the HR6 type compressor, I'm not sure how that would work.
Edit: The 88, I think, uses a different mount beneath the engine itself from the 86. The transmission mounts should be Ok. Also, the 88 uses a single serpentine belt for everything (no separate belt for the AC compressor), with a tensioner that is somewhat hard to find these days.