Well I guess my machine is out of service for a while. Y axis is missing steps even at low speeds. Belts are tight and it actually sounds like it’s skipping inside the stepper.
I don’t think I’m over or under driving it but unless I tear the machine apart to get that stepper out I won’t be able to look up the specs.
Sigh 
Might be some teeth are chewed on the belt?
Issue resolved! The acceleration was WAY too high in the config. It was ramped up to 10k while we were working on tuning and apparently this machine is very unhappy at that setting. Dropped it down to 5k (default is 3k) and it hasn’t missed a step this job yet.
However it does look like my lead in/lead out issue is back where it doesn’t burn all the way to the boundary during raster