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So the answer is 

5.2.1 Initialization parameters
Set P02-31 to 1 to initialize the drive parameters, and the drive needs to be restarted after the setting is completed.

P02.31
0: No operation 1: Restore factory values (except P00/P01 group) 2: Clear fault records

So NO that does not tune the drive.
. 

7I96 + 7I85 configuration with step/dir index on 7I85
and PWM on STEP04 pin. DIR04 pin is left as GPIO
so it can be used as enable, direction, or whatever.

Hi RodW

Thanks so much for your effort.

What I have done so far to get my gantry moving is just tie the home markers for the 2 X axes together

net mydigitalinx lcec.0.0.mydigitalin => cia402.0.mydigitalin cia402.1.mydigitalin

I then modified the cia402.comp file to accommodate. I Use the index pulse from each axis for the final position. I am away from the machine until Friday, I will upload the files then.

I just loosen the coupler once homed to adjust the squareness. It seems to be working. (only need to adjust once)