Alright, I got my door lock situation sorted out. Before going on, I want to say that this worked for me, I am not going to swear this is necessarily correct. The specific problem was that the lock rods were under the front pivot bar of the window (the flat bar that is at the front of the door which the regulator pivots on, it has a raised portion that appears to be where he rods are routed). As it turns out (at least for me) is that the lock rods go around this bar and above the window regulator arm. When the window is rolled up, the arm goes down, thus it does not hit the lock rod. The door opening rod goes behind the pivot bar.
I am attaching some pictures and a drawing to help explain this. By moving the lock bar, it allows more movement and less friction on the lock rod.