It's sad I have so many problems. I was forced to buy it for $1650 with a faded-up hood, cracked windshield, but otherwise perfect (aesthetically and mechanically as far as I can tell 5k miles in)

First off, apparently I left my brake fluid cap off... :/

The door seals are all good, headliner is still spotless, and the problem is only when the car is sitting in the rain... there's no kind of leak when it isn't runing and the A/C *is*, so I assume that's not it.

Above the floorboard, covering up the stuff behind the glovebox -- there is a piece of carpet. I felt it, and it's soaking wet. The water leaks onto it and then off a corner into -- you guessed it -- the middle of the floorboard.

What's the most likely culprit up there?

Auto-X, couldn't find the cover you mentioned :-/

There is a seal similar to the door seals in the engine bay, right under the windshield. It wasn't attached, so I attached it -- but I assume that's just to guide water away from the engine.