Hi,
You said that the Y axis was accidently overdirven to the micro stop switch.
Have you taken the manual crank handle and moved the Y axis off the limit switch? If you manually move the Y axis off the limit switch and reboot the system it should work.
A few years back I had a Seiki XL CNC Mill with an Anilam 1100M Controller. I had the same issue but it was always with the Z axis.
If that doesn't work send me an e-mail to [email protected]
John