Car was like this when I bought it. As you can see, the previous owner "fixed" it with silicone. It still leaks in the rain, and the rust is getting worse, fast. I realize that the final window caulking should be done by a window professional, but I would like to take care of the body work myself. Can this be done with the window in place? Anybody else have this problem before?

Unfortunately, there is only one way to truly fix that rust. A body shop.
Your windshield doesn't have as much metal to seal on as it used to...
At the least it needs to be stripped, cleaned, and re-done properly without the mounds of silicone, which, wont fix a thing being stacked like that...
I've been there and done that with another bonneville of mine

eww, that is a pretty crappy silicone job.


unless youre rather savvy in the body work area i would just take that to a shop as there is ALOT of work involved with something like that.