Transmission Gear selector issues

The linkage is designed to work as a system. If the longer (lower) arm is what you had with the linkage you're using, then it's what you need to make it work correctly. I don't have a parts book for your year, but I'm willing to bet the 904s had different part number linkages than the 727s. Use the 904 lever, and I bet your problem goes away. As a last resort you could modify your arm (shorten or lengthen) to get the throw you need.
The issue is from mixing and matching parts... it can cause lots of different problems. But you're not the first:
Duster shift linkage | For A Bodies Only Mopar Forum
Guess I'll see f I can get ahold of a 904 shift linkage and measure the difference in there lengths. As far as the torque shaft goes the one I bought for a 71 A body 727 looked identical to the 904 one I'm using and it measured the same length all the way around.