Well the culprit of the great trunk leak mystery has been caught; turns out, the weatherstripping around the trunk lid did a really crappy job of keeping the water out. It was coming in near the trunk latch and dropping into the spare tire well. While I was at work today I asked my boss what he thought, and he said that was the best explanation. So they have the part ordered and it should be here tomorrow, and I'll get it replaced on Thursday when I head into work. They are also going to reseal near the taillights to make sure I don't have any future problems. I'm also having them look at my slightly rough idle, which I've thinking is the cracked plenum. They have that part in stock, so if that is the issue they are replacing that. Here are some pics of the really terrible looking seal on the ws:
