I did some work with 400E's and have can give you a couple things to try with your Y axis problem.
1. There is a file called stepperparms.exe that will load all the stepper parameters on the PCL IC's. Your y axix chip may have corrupt data on it.
2. If the above step didn't work and you feel comfortable with playing with hardware then pull out the stepper board and swap the y axis PCL chip with that of another axis(look in the manual under stepper board schematics). Run the above mentioned file and if the problem goes to the other axis then the PCL chip is shot.
3. If this fails I would next try the driver on the back door, again swap it with the X axis driver.
4. Lastly I would suspect the motor, you can swap it with the X axis motor.
Sorry, I can't think of a solution for the offset.
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