I still don't understand why the C88 board isn't working either....that board is simple, the input side is getting steps and dir signals but it's not driving either the master Y or the slave Y.
Using the C88 would free up the A axis to bypass the Z outputs causing the REV2 board issues.
Edit: Z in fact works fine on the A axis outputs. C88 still doesn't work to slave the Y axis drives together, but there are two ways to get it all working. Get pin 7 on the c35s rev2 working or get the C88 working.