Re: Manumatic lathe.
With the drives shut down LinuxCNC won't see the drives moving because the encoders are powered down. I'm assuming that you would be using the drive encoder output connected to the Mesa. It is possible to leave the encoders and drive control circuits powered up by feeding L1 & L2 separate from the drive main power contactors, but it is necessary to power down the control circuit and start it with the main contactors to so the drive does an orderly startup and keeps the motor from running away on start up.
The alternate method would be to use linear scales and use LinuxCNC as a DRO in manual mode if it will work that way and I assume it will. You should only need to do a reset to cancel any moves made in manual mode.
One small problem that you may have already considered is, by installing a ball screw on the Z axis it will pretty much lock up the carriage, much like engaging the half nuts. The way around this would be to connect the carriage drive motor to the carriage drive shaft and control the backlash with an air spring. That way you would retain full manual capability.
Sounds like a fun project.
Jim Dawson
Sandy, Oregon, USA