It sounds as if the OP is being very methodical about seeking out any and all points of possible water intrusion and has various ways of reattaching the mirror that will be satisfactory. From my experience, I would expect the window seal(s) to be the most likely place, but resealing the various other points while working on the problem is simply good practice.
I would also make sure when reinstalling the mirror itself that I used the sealing tape mentioned for the window reseal and also apply caulking/sealer around the mirror base and screws.
As always, simply my opinions and ramblings. Use the information as desired, and good luck.