Tom,

I'm having the same issue right now, by the outside corner of my driver's side footwell. Unfortunately as well, I already replaced the windshield and seal, and had a body and paintjob beforehand!

I replaced the windshield and seal myself (with the help of a friend), using bedding compound, but in all that arduous and messy job I wouldn't be surprised if some of it wiped off in the process. What I do know is that the leaking corner is where I had trouble fitting the trim tightly into the seal, and there is a small gap where it pulls away and allows the water to pool in that corner when it rains. I am thinking that is the likliest source of my leak.

At any rate, 3M Bedding and Glazing Compound, Part #08509 (in black) is what I used to install the windscrean, and it's what I used to fill the gap this weekend. It is sticky but at its driest is like a dense putty. It blends in unnoticeably w/the black rubber seal and can be shaped to angle away from the windscrean, like the seal is supposed to.

It seems to be working for now--I'll see how it holds up over time.