Those holes in the top of the door jamb are to let the mouse poop out.
Seriously, I think they might be for the cab assembly at the factory (maybe locating holes for welding the top of the door frame in place)
Is this an AD (47-54) truck? Those are seals for the windows and yes, they are hard to replace. If they're intact, I wouldn't worry about them. They're available from the usual suspects if you do need to replace them.
