Since fixing the door and sunroof water leaks I've been going through car washes and leaving it out in the rain and not a drop of water has showed up in the car. I have a paper towel 'trap' stuffed down in one corner of the unibody floor where I believe the water was coming in from the door leak and then draing down the side next to the seat and into the back footwell. The towel has been dry since I put it in there. So I felt confident that I had stopped the leaks and could put the carpeting back in in the next week or so.
Today I went to my dad's for Father's Day, and while there, we had a severe thunderstorm that went through with a heavy downpour. I jokingly said to the family that this would be a good final test of the job I did fixing the leak. Turns out it didn't stand up to the test of the heavy downpour. I had a puddle of water in the rear footwell again. But here's where it gets weird. I didn't notice it initially. When I got in the car, everything up front seemed dry. My paper towel trap was totally dry and there didn't seem to be any water. I do have the floor mats in the car just to catch road dirt off my feet but no carpeting. When I looked in the back I could see that I had a puddle. That was discouraging enough, but more so was the fact that by the time I got home just a few miles away, my paper towel trap was sopping wet and when I lifted up my floor mat, there were droplets of water all over the aluminum foil pad. Additionally, there seemed to be water around all the tack welds in the rear footwell. Could I be getting water from underneath or did the puddle, which wasn't big to begin with but enough to move around, move forward when I applied the brakes. It did appear that there was water in the weatherstripping at the bottom of the door opening and under the door trim again when I got home, so I'm not sure if that was full of water and drained out through as I was driving or what. I just can't tell where the water came in this time. Pulling the door apart and fixing the seal was fun the first time, but this is already getting old. And Andrew was right, there is water under the aluminum foil mat in the back, so I guess I'm going to have to try and pull that up at some point. Can that be replaced? Not sure where to source that. It must be there for a reason, right?

Edit: I'm 99% sure this didn't come from the sunroof. I truly think that one's been taken care of. But I'll double check that again.