I had the same problem after I replaced my cab seals for the doors. I used the push on type seals they are very thick and putting little round air holes about every ten inches helps the trapped air to get out and looks factory like.
I also had to take and remove the piece below the threshold plates bcuz the new seals pushed the threshold plate up to much causing it to rub on the bottom of my door, it was a very annoying sound and made it even harder to close my doors.
After trimming away the seal off from under the threshold plate my door striker plates had to be adjusted over again but this time it was much easier to adjust and now both my door's close flush and the body line's are straight now and both door's are locking up doing a double click and with normal pressure closing both door's.
I no longer have water coming into my cab from around my two doors.
Next repair will be both my window felt liner's plus both wing window seals and driver side window regulator then the Two Big Jobs front and back window seals. Praying I do them all the right way the first time especially the front and back windows.

Papa Smurff 63