Yes, you can use the same glue I mentioned on your other post for the window run felt.
There is no standard length to cut the seal where it meets the door seal. These cars were hand built, and each car was different. You simply have to "cut to fit", and to a point to where the door seal presses up against the roof rail seal at an angle when the door is closed. Use your old seal for a reference as to what angle and direction to cut it at. This is the very last thing you'll do. Don't do it before you put things back together.