TFT,
Keep working at it and let us know how it goes. I have a Taig mill and a while back I was working on trying to get rid of .003" in the Y. I played with every setting, tried the 50/50/50 rule and never could get the backlash compensation to work, the motors always seemed to be loosing steps. Max speed is only 25in/min. Ultimately I just replaced the Y screw and nut. So far it has been working fine. BUT, I still want to get the backlash compensation to work for it will help as these nuts and screws wear. It may also be my motion controller, I might have to try another. I may go that route anyway because this one has a shift button issue where it will think the shift button is still depressed when it is not. I am using a USB, Leafboy77 board.
I like the USB setup, and don't really want to mess with a parallel, unless they are plug and play as this one pretty nearly is. Ethernet is also a possibility.