It's been a few months but by no means is this project abandoned. As the project is coming together, I wanted to share some of the key hurdles we had to clear to get things moving.
Firstly, after we got the digital potentiometer issue solve we were happily running it back and forth. Then we noticed the y axis would catch some times. It seemed to be getting worse. Looking into the forums, we saw people pointing and the cheap rails we were using and we thought we may have to bite the bullet and upgrade. We tried copious amounts of oil and the stickiness remained. It seemed to be coming from the left side so we ordered 1 Hiwin rail and the project seemed stuck. Then Doug got out his fine tooth comb and went through the mechanics. Turns out we found some friction in the following location between the slave pulley and the spacer bracket.
We had designed in one brass bracket but we got some bearings (not shown) and we put one on either side of the pulley. The outer bearing interfered with the pulley so we added another spacer bracket. In any case, it working very well now and we do not have to deal with the slave motor.