Hi Tom,
My machine is using the nMotion board as the control board. I believe this came in the newer versions of the PM-940-CNC.
I have no experience with the nMotion board but let's see if we can make it work. Here's a few suggestions that you can try. Keep track of the changes you make so you can revert back to the original configuration if necessary.
1. On the nMotion Status and Config screen lower left corner there are check boxes for homing switches. Put a check in the X, Y and Z boxes and see what happens.
2. In Mach3 configuration Inputs screen change the Port# to Port 1.
3. Your limit and home switches are connected to Pins 1 thru 6 on your controller. Mach 3 recognizes pins 10 thru 13 and pin 15 as inputs. It appears your switches are not wired in series so you don't have enough input pins available for all your switches. You can wire them in series then connect them to two of your input pins (one pin for limits and one for homing), then change Mach3 configuration to reflect the pin numbers you are using.
Let me know how this works out.