Right, I cleaned out that area pretty well. The passenger side drain was fully blocked and the well it sits in had about an inch of dirt and muck. I removed that, and then with a coat hanger fished out what I could from the drain. It seems to drain perfectly now. I also poured about 20 oz of alcohol, dish soap, and water down both the driver and passenger drains during the process, which I think helped loosen the gunk that was in there and allow me to fish it out a little more easily. Both drains now drain plenty fast.

I added a baffle to the AC inlet too. Not enough to completely cover it -- just the bottom half is covered now so that I still get some airflow. Still, it should provide some protection in case the drains are too slow.

I might later fab some screens for the drains to help prevent subsequent blockage. I was thinking 1/8" mesh?

Anyways, do you think I should go all-out and remove all the carpet, amp, etc. to search for water? I'd hate to burn a day doing that only to find that I was OK in the first place.