I finally got my Shopbot PR upgraded, with a new gantry and Z axis.  Today I finally connected the motors and installed Mach 3 and the Ascension 1000 controller.   I installed the .xml files and .set files provided with the Ascension controller, and followed the set up instructions.   Here's my situation:
My X axis, both X1 and X2, work OK.  The jog command moves the gantry as its supposed. to.   The Y axis does not respond to the jog keys.  The Z axis does not respond either.  
When I swap the plugs at the back of the Ascension box, sending output from the X axis to the Y or Z axis, both of these axis work.  This suggests that motor and cables for both are OK.  This leaves either Mach 3 settings or a problem with the Ascension box as possible troublespots. 
 need help to determine if I have some setting wrong somehow, or if I have a problem with the Ascension hardware. 
Thanks so much for this forum.  I look forward to learning Mach 3.  
Wayne C