Before I take the plunge.....
Can  the inevitable tolerance error in ball screws (matched pair) i.e travel per rev, be overcome by calibrating travel and setting parameters accordingly on each side of the Y axis? Put simply will the software accept different parameters for each stepper motor when in the master/slave relationship or will the slave stepper motor 'receive' the master stepper motors' parameters.
Thanks.

we do this all the time mechanically, though I'd expect we'd have the same issue if the ballscrews ran at even marginal pitch differences. This must be a fairly large machine to require two ballscrews or were there other mechanical or electrical considerations? Precision matched ballscrews are designed to run at extremely low tolerance differences.. i'd expect in the 0.00002"/mm range or better. whats the rating on the ballscrews and whats the maximum travel distance. and what machining tolerance are you trying to hold? Bob

Thanks Bob for response.
I doubt the ball screws were ever marketed as 'precision' ... just matched pair.
If I was to calibrate (motors) each side of the Y axis to travel would Mach4 Hobby accept those parameters. Parameters would obviously be different for each motor (due tolerances of each ball screw). Some control softwares do not allow differing motor parameters on Master - Slave arranged motors, the master motor parameters get given to the slave. I suppose my question should have been - does Mach4 support different motor parameters on Y Master and Y Slave as this would overcome any ball screw tolerance difference.

if its running as a slave axis, i would think it accepts the slightly different calibrations. Master/Slave is a normal operation mode, and you would expect each axis to have separate setups, backlashes, etc. Some of that may be part of the motion card you're using, and not wholly in Mach4. You probably need a reply from someone deeper into Mach4 than I am. Bob 

Inside MACH you slave motors together, and the answer is yes.
You can have different tuning parameters for your master and slave axis.