problems with Y-Axis, elliptic deviations after several changes -Probe Basic V.5

Are you dropping packets? that is, what is:

hm2_7i76e.0.packet-error-total

A dropped packet will result in a (bogus) following error spike,
as stale stepgen position (from the previous cycle) will be compared
with the commanded position. At a 2 ms servo thread period and 125 mm/sec
velocity, a .25 mm reported following error value is possible from a dropped
packet. Note the this does not mean that there is an actual path deviation
of this magnitude, this is bounded by the max_error PID pin to ~.0127 mm
per dropped packet.

I still think the physical error is most likely mechanical as it only shows up on Y.

To diagnose stepgen errors, the best thing is to plot the following error
with halscope like this:

 


Note that this is in inches but the velocity and acceleration are about 4x and 6X you machines values
and the inherent stepgen error is less than  0.25 micron.

Another possibility if the system latency is really bad, is loss of DPLL sync, so you might try increasing
the DPLL time from -250 to -500 usec

 

Also are those things correct for your steppers, they look big to me.