Need door seal/alignment advice

[bigsky]

Finally getting 72 K10 put back together, after many hours of trial & error door alignment. I got the gaps all fairly uniform. Problem is Pic #1 the rear of the passenger door is out about 3/16". This is with door seal installed. Aligns perfect with door seal removed. What is the best solution for this problem. I did replace the door sill/rocker, could this be holding the seal out? I have adjusted the striker catch plate in as far as I could, without slotting the holes.