Touareg :: Rattling Noise Inside Cabin - Doors Not Sealing Properly

I have grown extremely irritated over rattling inside the Touareg and decided to listen closely in an attempt to identify the guilty panels or whatever is causing all that noise that makes the cabin of my 2004 Touareg sound like the interior of a 1994 Ford Explorer with about 200,000 miles on it.
I identified the rear seat bench as a noise generator a while ago. I wrapped electrical tape around the latch bolts, but that didn't work too well. It seems that the rear middle arm rest rattles quite a bit in itself. The rest of the rattling seems to comes from the rear seat backs, but this is old news.
I noticed that the door panels (or at least that's what I thought) on the driver's door and right rear passenger door were rattling and creating a lot of noise. However, as much as I tried to hit (lightly) the door panel with the palm of my hand on different areas of the door panel, I couldn't get it to make the same noise.

After listening closer while I drove, it sounded like the doors themselves weren't quite closed. They sounded like they rattled on their latches. Something like taking off with a door ajar, but the noise isn't as pronounced. Then I remembered that every once in a while, during a visit to my friendly local car wash, water was entering my vehicle and accumulating on the rear seatbench. Upon closer inspection, I would notice that the water was getting in easily between the rubber door seal and and the door sill.

Two days ago, I decided to check something, and low and behold, I think I found the problem. Those two problem doors don't shut as tightly as the other two silent doors. I ran my fingers along the door crack near the door handles on all four doors and discovered that the two noisy doors "stuck out" some. Just a few millimeters (maybe 1 or 2 at most). I then tested it with a flat edge and it was even more apparent. I then stood behind the vehicle (far rear left and far rear right) and looked straight down the vehicle's edge and noticed that those two doors were sticking out.

I tried to loosen the door latches on the door sills to move the latches in a little, but I found that a T-40 torx is too small and a T-45 torx is too large. In fact, the T-40 worked on the top bolt on both front door sill latch hooks, but would strip the bottom bolt on the same door sill latch hooks. Those 8 point bolts are not torx (duh). I'll have to wait till Tuesday (Monday is a holiday here) to get this rattling fixed. I really hope that this eliminates most of the noises I am hearing. I notice that the front right door doesn't make any noise, and I also notice that that is the one door in the vehicle that needs to be shut extra hard in order for it the shut the first time. If it's not shut hard, it usually takes two or three tries to get it to shut. My 2003 GTI did this as well, with the very same door.