I just replaced the roof rail seals(SoftSeal) on a 69. The car did not have any when it was bought so I dont know exactly how the door glass is supposed to go in. With the door shut is the glass supposed to go inside the "U" on the seal or outside. I assumed inside the "U" but I cannot get the window adjusted where when the door is shut the glass goes inside it. It does fine on the top part it is the angled part of the glass that I am having problems with. No matter how it is adjusted the glass wants to catch the seal on the way in. Usually toward the bottom 4-5" of the angled part. Any thoughts?

Stacey,
I don't know any magic tricks, but as you suggested, the glass should brush past the little lip, and seal against the big lip in the "U".

I "fiddled" with mine, until I got it right. First, I got the angle right so it would seal along the front and top of the glass. This is done by adjusting both the glass and the stops. Don't forget you can adjust the angle by moving the bottom of the glass in and out.
Then I got the quarter glass to fit to the door glass. again, I had to adjust the angle on the quarter glass to get everything to line up right.

I spent 3 hours on the one side, and due to the learning curve, or luck, I did the other side in less than an hour.

Oh, don't forget, there is some adjustment in the roof rail itself. I installed the roof rail sort of loose, then inserted the seal without glue. After everything was aligned properly, I put soem tape in a couple of spots to mark the position of the roofrail, then pulled out the seal and tightened the roof rail. Then replaced the seal. I used no glue, even the second time, although I probably will glue it. I have one mint original seal, and one aftermarket. I'm holding out for a mint or NOS one for the other side. Ah, to dream.

Stacy, In the Fisher body trim manuel, there is a section on glass adjustment, if you do not have one, you can obtain one from one of the vendors like Ground-up or Ricks, about $30.00. The glass can be moved in/out & end to end. Read carefully its fairly self-explanatory.

The one thing I did not think of was the adjustment on the roof rail itself. That little bit of adjustment will probably be enough. Thanks.