Misneachail

I experienced a bizzare failure of my alternator this past weekend. Flashing dash lights, chirps, buzzes, window wiper failure etc. with finally my car dying in a torrential rainstorm, stuck in park on a busy street.
(My driver side window had started slowing down a couple days before this and the major problems started before the rain started)

It was towed to my daughter's work (she's a mechanic) where she was able to replace the alternator for me today. I discovered that my window auto-up doesn't work & neither does my covertible top switch. I can roll the windows up by holding the switch, but they will go down automatically. This means when I park my car the windows won't roll back up into the top, leaving a small gap. (This happened once before, but seemed to resolve itself after a week or so.)

Im sure my daughter can fix it, if we can figure out what/where the problem is. Is it possible for a failing alternator to short out the switches or top motor?
I'd really appreciate any help or suggestions you can offer.