Reporting back, and have found some interesting things.

Checked the sunroof drains, everything appears clear. Checked the windshield cowl cover and discovered that the drainpipes were pretty blocked up, which would allow water to stand in the cowl. I also purchased a replacement cabin filter, and so removed the cowl and discovered a second set of drain pipes when water gets under the cowl. On the passenger side, next to the cabin filter intake, there was a bunch of leaves and debris that indicated there may have been standing water there. Cleaned and cleared everything out, thinking that standing water right by the cabin intake may have caused some of the issues.

I went around and examined all the door drains, a small hole at the front and back bottom rim of the door. When I got to the driver's door, I noticed that there were no holes visible, so I took a dental pick and pressed into the paint in the locations I thought the holes should be. The pick pressed right through the layer of paint into the door. I spent some time clearing out all the excess paint to discover that there were holes being covered. I'm not sure if the door came like this from the factory, or if was resprayed at some point, but for whatever reason, those holes were covered. I removed the door panel and noticed that there were water lines on the bottom of the door indicating there was standing water perhaps 1 inch deep in the bottom of the door at certain points. I also noticed that water marks were leading down the inside of the door wall from the door handle. My guess is that water would seep into the door during rain, and pool in the bottom of the door. Perhaps this also lent itself getting moist inside the car, although I'm not sure what path it would have taken.

So everything is cleared out at this point and I'm waiting for some rain to see how well it fairs. Hopefully one of those two issues will fix the problem!