Thanks for all the replies!
I spent this past Saturday sealing the front and rear windows on both the window and body-side of the trim moldings. Compared to older cars with chrome trim, it is more difficult to do the post-sealing clean-up, as the silicone tends to stick better to the rubber molding and running a razor blade on the rubber trim can easily carve out large chunks. I also sealed the gap between the door trim and the roof--seeing as how this may have served as a drip rail, the jury is still out as to whether this was a good idea.
Thanks to backnblackz06's tip, I removed my wiper cowling and took a look by my wiper motor. Yup, there seemed to be a gap in the bond along the foward seam and also down in the wiper motor well. I was able to seal both areas using silicone sealer and with the help of a small, disposable "flux" brush, which I used to force the silicone into the seam cracks. After allowing the silicone to cure overnight, I trimmed excess from the windows then proceeded to flood the car for a leak test. So far it looks like the leak is fixed!
Another thing I did, to help the wiper motor well to drain, is to flip half of the drain tube's flaps open. To best describe this, picture a condom--
--if the tip had a large X sliced in it, that would be like what the bottom of the drain tube is like. You can flip half of that X inside-out, so there is absolutely no restriction to water drainage from the tube, especially if a large volume of water is trying to drain.
I also ran a bead of silicone under the front and rear edges of the interior door trim to help seal and form a raised barrier to water intrusion from water getting past the door seams--if water can get in the door area by the door sills, it is easy for it to flow under the sill and edge trim and get into the carpeted area. Hopefully this works--I still have to test this part of the sealing more. I had noticed that I would get a lot of water dripping from the seam between the door sill trim and the piece behind it, leading me to speculate that water was getting under the trim piece at the top rear of the door and flowing down.
Hope this will help some of you do an at-home fix, too. I know I was dreading having to take the car in to the dealer--even if it was covered under warranty.