Hey, I just took one off a junkyard truck a few weeks ago and I'm pretty certain the rear window seal, i.e., seal between window and cab, is just a standard rear window rubber seal for your specific truck.
Unless yours is severely damaged, I doubt water ingress is coming from this seal; other areas for water are likely the felt seals or if the plastic frame is damaged.
As I recall, the custom plastic frame is molded to fit into the standard rear window seal and a custom window slides up/down into said custom plastic frame.
Also, I still need the motor for mine ... if you wouldn't mind, can you take a pic of the motor that drives the window? And advise if there's any identifying marks?
Thanks and good luck,
Carl