Adjusted motor tuning, its fine now. moves and is happy. Still need to tweak the y a little.
It does seem that tuning in the omron software is not *quite* the same as running under position control. Didn't lose anything, just small tweaks. X was the howling one and it still tracks within 3 microns during acceleration. The Y has 2 microns lad in straight motion and 6 during accel. Bigger motor and MUCH more mass. Just trying to keep it "stiff" as possible. Anything under 10 microns during accel is a win. (this machine does high speed surfacing).
Anyhow, break time, I'm very happy. thanks for all the uh.. moral support?

hahah. I get frustrated a lot when the instructions are missing big blocks of important information. I think I need to write a "ethercat setup for dummies" post so other people can follow something a bit more straight forward. The "implied prior knowledge" is what really turns people away from linuxcnc in general.