So after your comments on encoders I'm thinking SSI absolute encoders would surly make things simpler. But that means getting a different board to read ssi. changing them out on the motors is no problem but for the cylinders I would be making a belt/pulley system to make them linear as absolute linear scales are way out of my budget for this. I'll have to call and see if the 7i96 will work with a 7i74.
here is a link to the encoders I've found.
encoders
also wondering if you couldn't call a single axis out in gui. pass that command to two separate axis (the cylinders) in velocity mode. hijack the velocity out command number (say max vel 65) into two position commands for the steppers. wouldn't linuxcnc keep the two cylinder axis in sync by adjusting the velocity for each cylinder witch would in turn change the position of the steppers running the valves? Or I'm I talking crazy?