Well, I was tearing out my carpet and the floor was all pretty perfect (even the original paint and chalk marks), except for some pretty bad rust behind the passenger seat. I can see a spot where it rusted all the way through.
That's not the worst part, the paint on the roof is cracking directly above that area. I didn't think much of it since I had the same cracking on the tailgate and it was just because the paint is old and thick. Now I am wondering if my Elky originally had a vinyl top, rusted though, and was patched with bondo before the last paint job.
I guess I'll have to remove the paint from the roof. But, I'm afraid of what I'll find.

I'd say it would be quite a bit easier (and LOTS less work!) to drop the headliner down and see if there is evidence of a roof repair. If you go through the paint to see, it will need a repaint now regardless of what you find.
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It needs paint now anyway. The paint is old and it needs a new tailgate and fenders at a minimum.I should probobly drop the headliner anyway though since the guy who put it in didn't know what he was doing and it's all screwed up.

Most likely place for water to enter the pass compartment is the corner of the rear window or where the bed meets the back of the cab. Pull the inner storage plastic box out and check the right side for stains with a flashlite.Might not find the source of the leak but at least you won't screw up your paint.

71350ss is right; my El Camino (a 78 model) has had leaks at both of those places. Mostly the seam where the bed meets the body. Sealing that seam with regular body seam sealer almost completely stopped the problem.

Also, parking the car nose up on a slight incline, just enough to where water runs rearwards in the bed instead of pooling in the bed right behind the cab, is a real smart idea.