So I think I may have found my issue.
We started out with our cncrp plug and play kit about ten years ago, and we stayed using the parallel port. At some point we needed to replace the control PC and parallel port is no longer really a thing. So we got an Ethernet SmoothStepper and all was well. We then eventually added a spindle and the PMDX 107 control module. Well when the spindle was installed, the ESS was never powered independently. Apparently the PMDX 126 can not power both the ESS and the PMDX 107 simultaneously. So I have added an appropriate 5v power supply just for the ESS, hopefully that will finally put this to bed.
After supplying independent power to the ESS, I noticed that the X axis is running more smoothly already, as it was kind of jerking along before.
Looking back on the last few months, we have had a lot of really random things occurring and I hope this was the cause.
Thanks everyone for the help!