ok, I accidentally hooked up my neg battery cable to the pos. bettery terminal, and the pos. battery cable to the neg. battery terminal. This was do to all black wires since I relocated my battery to the front.

Anyway, so I hooked it up and it took me a couple minutes to realize what I had done.
The lights went up when turned off, and the lights turned on when they went down, and off when they went up. Just as I was about to unhook the cable to test my theory, I noticed a grey smoke oozing out from under the passenger side dash. After switching the battery cables, everything appears to work except for the passenger side headlight motor. the light turns on, but the motor doesnt go up. This is an 88 coupe, and I just completely disassembled the healights and motors and cleaned and reassembled. They were working great.

Any ideas what the smoking would have been?
something to do with the headlight?

If you are lucky you blew a fuse link, but they are in the LF under the hood.

what does LF mean?

left front

The damage that occurred depends on what was connected and what was turned on. If the key was off, you will be better off.

Was the alternator connected? If so, you had a direct short across the stator diodes in the alternator. You very well may have a failed fusible link "E" (near the battery). You should check that.

Also, any relay that has a freewheeling diode internally connected across the coil would "look" like a short circuit to a reverse-connected battery. This may also clear a fusible link.

Still, the question of what "smoked" under the dash remains. Again this depends on whether the key was in any position other than off. If you can answer this, it would help.

I had the key in the on position. The radio and heater etc. would not run. It was not in the Acc. position. Also, I had the alternator wire disconnected.

The size of the link is imprinted on the side of the plastic butt connedtor at the link, likely 14 guage, but not postitive. Napa sells fuse link wire, USE THE CORRECT SIZE! The link should be 6" long.

what do these 2 fuses protect against?

I don't have my drawings in front of me, but basically everything except the starter is protected by some sort of current protection.

It is not a good idea to elliminate the fusible links. Were you to develop a short to ground in an unfused wire, your Fiero is quickly going to become a fire statistic.