It seems as though the water is coming in through the roof ... all
four corners are completely rusted away and it's like stepping into a
rainforest when you get in the car on rainy days (an inch of water in
the cabin and super humid).

We're going to bondo up the holes we can see this weekend, but is
htere any other place we should check? Going to look around the hatch
seal next.

I know it's not coming in from flooding because where we park it
doesn't flood, and we have several other low slung cars that would
flood if that were the case.

And I've been in the car and had water dripping out from the passenger
side roof handle as I sit there.