Found two leaks. Top portion of the rear window and top of the passenger quarter. I can see two water trails down the glass now that everything has dried out. So based on the volume of water puddled in the car, this probably means it is leaking from the bottom as well. Fun times.

Looks like I'll be attacking the seals from the inside with RTV. Really don't want to do it the proper way by removing the windows to reseal them unless I really have to. Gitter dun.