[Fiddlebog]

Are you sure you're getting the relay back in all the way? That big thing takes a fair bit of force to pop in.
Any problems with the convertible top function? Or is it just the windows?
I definitely didn't replace any electrical parts when I was fussing with he '99 (the one that had the problem). I did have to replace a few fuses, though I don't remember which ones. I also recall having removed and replaced(not a new one) the convertible top relay for some reason. I probably sprayed the contacts with some QD contact cleaner, since that's my standard practice when removing electrical components. Maybe try that, then make sure it's really in there good.
I had a friend help me with some of the work on that car(his car now), but I don't think he was around when I did the electrical stuff. I'll ask him if he remembers anything about it. I apologize, I don't know why my memory is so fuzzy on the subject.