In case anyone was wondering. I was able to figure it out. After hours of teardown I determined that the geometry was off on the trucks that I was using on each tower; there was too much flex and it caused an excessive amount of bowing on the arms, resulting in effector tilt that I could not see when it wasn't moving.
I did not want to go back to the SeeMeCNC trucks so I finally found the, now defunct, trick laser trucks. I searched around the internets for a while and found the cad model for them and tweaked the mounting holes to have the proper geometry for Hayden's ball-cup arms. We're back in business.
The ripple that I was seeing before is completely gone!