Is there anything you need to do to prep the bondo for primer? Also, I have lots of good paint left on the truck, I know you can paint over it, anything you need to do to prime the paint? Or can you just paint over top of the old paint without priming it?

Also, how does a guy get at the clearance lamp wires in the roof? I want to replace the harness if possible...

just make sure your filler is smooth. there is an etching primer for bare metal you should apply first and then a grey filler primer on top of that.

Painted metal is OK to paint over directly as long as it is in good shape and has been wet sanded with about 600 grit. This will scratch the surface enough to allow the new paint to adhere.

Before wet sanding I would wash all the paint down with mineral spirits or some such to get rid of any old wax grease whatever .