From the above document, it looks pretty standard. Pins 2/3 are the X Axis (Pulse/DIR), 4/5 are the Y Axis, 6/7 are the Z Axis, 8/9 are the A (4th) Axis, and Pin 1 can be used for the Enable signal for all if desired.
For the limit switches, pin 11 is the Z Axis limit switch input, pin 12 is the X and pin 13 is the y. E-stop is on pin 15 and pin 10 is available to use (possibly for the tool probe). These are all referenced to the parallel port numbering. The "Interface" numbering seems to be the board pin numbers for the actual hook-up internal to the control box.
For the limit switches (also doubles as the homing signal) four wires are needed. The first is connected to a ground (GND) pin on the board and connects to all switch signal legs. Each axis would then have two switches (or three if there is a seperate homing switch needed) which return a signal to the referenced pin. My preference is to wire the switches for each axis NC in series for safety purposes as a broken wire would be detected this way. You would then configure Mach3/4 for an active HIGH signal (uncheck the active low check-box) for proper operation.
Stephen "Highspeed" Kruse