BP retrofit yaxis drive burnup- follow-up

I'd like to give some follow-up on the complete reworking of my BP
retrofit. I was burning up Geckos on the y axis. The installer
originally put in everything on top of all the original BP CNC
equipment. I gutted the cabinets and rewired everything. Just tried
out the machine and everything works almost. The relay for the DC
powersupply that had been on the DC side got switched to the AC
side. With switching on the DC side there was always a "bump" of
the motors and the backup powersupply for the computer sensed a
spike and briefly shutdown. Now with the AC side switched there is
no bump. Hopefully the electrical problems are behind me except for
the fact that the x axis will not run smoothly. It stalls unless
tuned for very slow speed. The y and z axes run at top speed and
acceleration in Mach2, much better than before. It looks like the
wires are all connected properly but I will recheck everything
tomorrow. In the old configuration the x axis always ran fine.

If the wiring is fine and the capacitor across the power on the
Geckos is not bad, what next?

Thanks for any suggestions.

Keith Clark