$65 isn't bad if they fix all your wiring.
when you say you tried connecting the loose wires, were you able to match each pair of the same color wire and stripe colors on the wires together? start with one single problem first. for example, if your tail light's not working, trace the wiring starting from the fuse all the way to the tail light bulb. if the fuse is good then i'm sure you'll find the wiring broken somewhere along the path from the fuse to the light. note what color the wire is from the fuse block for the tail light, then trace it as much as you can until you're at the area where the stereo was. if there's a problem with that wire it should be here. can you see where it's torn? use this debugging process on everything else that isn't working. but i'm guessing most of the problem is right there in the dash where everything was ripped out.
if you need the wiring diagrams still, pm me with your email and i'll send you some scanned copies from my 94 repair manual, the same as the 93 4runner.