Keep in mind this is just my opinion.
" A small silver dollar size piece of primer and skim bondo lifted and I picked at it and popped it off. Metal was clean anbd bright underneath but, the bondo flaked."
It would appear there was something on the metal to keep the filler from bonding to it. It may be just that spot or could be a problem in other areas.
If there is rust coming through the primer you are going to need to sand all the primer off and take it back to bare metal. If you are going to use 2 part epoxy primer, my opinion would be get all the old body filler & rust off the metal, clean it with marine clean then cover with the epoxy primer, re-do the body work, prime,seal & paint. You can also put the body filler on the bare metal & then prime it. It depends on how much money you want to put into it and what you are looking for when you are done, a daily driver or a show truck.The only reason for the marine clean is you don't know what the PO did that made the body filler not bond. That will take off all grease,oil etc. I personally would cover the back of the metal where you can with POR-15 to keep it from rusting through from the back side where it was welded.
Got any pictures you can post so I can see what it looks like?
