["QUICK-SILVER"]

Scott,
The pics pretty much look like any other car that melted fuse links. Just looking I'd say you'll want to add a junction block to get rid of all the clutter on the back of the alternator, but that can wait for now.
The dead battery, no start situation that happened, is all the more reason to check out the burn area at the tube. Along that same line of thinking, did you try to crank it when the wires smoked under the dash? If the purpe wire is shorted out at the tube, wires could've smoked behind the switch while trying to crank it.

The melted fuse holder to the fan obviously overheated. You didn't say if the fuse was blown or not.

The fuse condition and the key on smoke (crank or not) is just a couple of more pieces of the puzzle that'll help trying to figure out what happened or what's going on.

There's more but that's enough for now. Just trying to narrow down possibillities.

Clay