well I may have done my victory dance prematurely. I went to start tuning mach3 today and the motor was very jumpy and eventually faulted out. I reset the drive went back to the tuning software and tried running the same exact test as the one in the video and I'm now getting around a 750 pulse error and I can hear the stepper making a funny noise. I checked the coupling connecting the motor and ballscrew to ensure it was not slipping and it's not. I also reconnected the original encoder and changed the encoder count back to original and it works fine again.

My next though was maybe the tape wasn't aligned to the sensor since I had jogged the machine down maybe an inch. So I disconnected the ballscrew from the saddle and ran the saddle up and down the entire travel and the green "go" light stays on the entire time.

Any idea what I could look at to start troubleshooting?