I was replacing the alternator after a test and did not put the positive back on before I put the battery back on. There were sparks and smoke, but I didn't find a burnt fuse or a melted wire. The only thing that comes on is the headlights and the charge light on the dash.

I'm afraid you burnt a fusible link. Should be in the under hood fuse box or near the battery positive post. It will have 80 or 100A ALT on it. It could also be a fusible link wire that comes directly off the positive battery post.
Memory is not serving me correctly on the '85 model. Too long ago and I have CRS :).