I all ready did that and tested it with a dollar bill. I think it helped a little on the driver's side but a little concerned about doing it anymore on the passenger's side. Just couldn't get a good even pressure on the whole window frame with the dollar bill and the window frame looked like it was going to buckle on me one time so I stopped.
I redoing the finish on the truck and will be doing most of the door jams with bedliner. The stuff I'm using won't be too thick (about as thick as an index card) but may do the trick. If not I replace the weather stripping, try realigning the door (which it all ready appears to be square on) or do what the previous owner did.

 

New seals form LMC.....?

 

New seal in LMC run about $49.95 for the door weatherstrip itself. The drip weatherstrip, which goes along the top of the door is $19.95, that catches the water along the top and forces it down to the mirror, the rear door seal is also $19.95

Pretty cheap to try it out, at least you rule out the weatherstripping as the culprit for under $100. Then you know its the door and its alignment or un-alignment...

 

I out all new seals on mine when I reapainted it as seals were worn all around, and nearly destroyed at the threshhold on the floor. Not only does it seal out all water, it eliminated all the wind noise. A good investment in my opinion. Can't stand the wind noise.