I am glad you have found many of your leaks. I have a '54 Cruiser with all the Hehr windows. I am a little confused/concerned because I haven't witness any leaks with mine and I have barely caulked anything yet, since I am in the middle of polishing. I installed new glass and weather stripping on the outside as you did, and i agree that exterior window seal is probably not a good defense against water. But I didn't believe that it needed to be...
My concern is that I thought that the window drain caps did most of the work in keeping water out. Did you actually vulkem the window pane to the window frame? Inside the keeps? A PO did this to a mangled window, and I found it a rather crude fix. It seems that originally something was working without such a seal.
Please excuse my rambling.
After reading this I just assume that all of my windows should be leaking!!
I have had the windows wide open in hard rain with no leaks so I am surprised to read about water coming in around the glass.
Yet I have only had my 54 for a few months...guess there are plenty of time for leaks!