First, thank you all for helping me as I am in a bind.
I am painting a 1971 Eriba Puck. It is a small German camper meant to go behind a VW. It has a fiberglass top, and is skinned with thin aluminum (not like and Airsteam, more like a pop can). I replaced a few panels of the aluminum and repaired the rest with some filler. I sanded the entire thing with 80 grit and got it ready to prime.
I had a guy who paints trucks for a living (and does restorations on the side) come out to advise me about the aluminum. He recommended a self-etching primer over the whole thing, then 3-4 coats of a urethane high build primer. When I went to the paint store, the guy told me I can't use self-etching on fiberglass. So he recommended an SEM direct to metal product. I severely underestimated how much primer I would need. I saw how quickly I was burning through it and changed my plan. I primed all of the new bare metal panels and one side of the camper that included an old panel with the original paint. I spot primed over the repair area that had bare metal showing (again, all aluminum).
I called the paint store to see if I could get more primer, explaining what I had done and how much more I needed. He paused and said, "You sprayed this over the original paint?!?!?" Now he says I can't do that and I need to take it all of, and get all of the original paint off. I think the paint is a lacquer, as it softens with lacquer thinner, and I can rub it off to bare metal with some work. The original pain is very thin.
Then I listened to the paint guy for about 1/2 hour, going back and forth, confusing me more and more as we went. He went from telling me to bury it all in epoxy to sanding it all off and just going right to paint. I was really hoping to use a high build primer to even out the flimsy metal a little bit...
So, knowing all of that, what would you recommend?
Thanks again,
Dave

You are dealing with two different materials here, and they require different primers.
Use epoxy primer on the fiberglass top, after stripping the lacquer or whatever is on there.
The aluminum is a different animal. It starts oxidizing immediately after any coating is removed,
and the resulting corrosion makes it hard for any primer to stick. A zilnc chromate primer is
best for aluminum, but it's hard to find in some areas because of EPA regs. An etching primer
will also work fine, although it won't have the sacrificial benefit of zinc chromate if it's scratched.

Some people here have used epoxy primer on aluminum, but I have no experience with it on aluminum.

After the direct to surface priming, you can go to the high build polyester primer for finishing.

Unfortunatley I already hit the bare aluminum with the epoxy direct to metal primer. The issue is worse now as the primer lifted the original paint, though only in a few spots.

The question is really what do I do now, not what should I have done.

Well, the lifting didn't get any worse overnight, but it certainly didn't get better:)
I decided to just sand it all off (except where I had primed over bare aluminum. All of the original paint will now be removed.
Then I will reprime with the direct to metal primer, then a few coats of the urethane high build primer.
Does that sound ok?

The epoxy is not causing your problems, it is the lacquer based paint.
If you want this to turn out right you need to strip that lacquer base paint and be sure it is all gone.

Just curious, is the primer called SEM 'Metalock' DTM?
If so, SEM says it's for steel, aluminum, fiberglass and SEM, sort of an
all inclusive primer for everything. They also say it's a high build sandable
primer.

So according to SEM, you can prime both the fiberglass top and aluminum
sides with the Metalock. And also use it as a high build to flatten out the
sides a bit. Since you already have it, that's what I'd do, just spray multiple
coats of it and block sand until satisfied with the work.

That's after stripping all the existing lacquer off, as 68 Coronet R/T said.

Yes, it is SEM Metalock.
Unfortunately it is pricey and my paint supplier doesn't have it in gallons. I switched to a different DTM epoxy after stripping the whole thing. I am heading out to prime it this morning. Wish me luck.