After recent rains, my new purchase '79 has damp carpet in the rear footwell. Where do I start looking? Is there a common leak area?
Back window? or seams of bed?

I don't think this is from the door window or blowing rain. The car has a good cover that would stop blowing rain from pushing past seals, but the car does get damp. I am leaning toward leaks in the bed because the cover does sag and forms a baby pool, allowing plenty of water to still get into the bed.

When I test for water leaks, I always start at the lowest point and work up. In your case I would have someone on the inside while you run a hose in the bed on every seam. If you don't get a leak there, start working your way up until you locate it.

The rear window is notorious for leaks. To test remove the inside trim and have someone run water around the window. Another place they leak is at the quarter glass, usually the lower weatherstrip. Another place to check is at the A pillars. Sometimes they leak at the windshield sealing and the water runs down the pillars and ends up behind the seats which is a low spot. If you inspect the sealing it usually has dried out and shrunk and this is what causes the leaks.