Hi John,
Limits and Homes are input signals.
Limits are X++,X--, Y++ etc, disable all of them to start with. If they are disabled it doesn't matter what pin is assigned, but suggest you put '0'
as the pin. Pin 0 doesn't exist.
Homes are X Home, Y Home etc disable all of them to start with and assign them to pin 0.
Your Estop should be port 1 pin 13, or at least that's the pic you posted. Try Estop active low. Fire up Mach and see if the Estop button works.
If it doesn't try Estop not active low and try Mach again. One of the combinations should work if your machine is wired with the Estop wire
going to pin 13 on your BoB. If not you're going to have to trace the wire from the Estop to the pin on the BOB.
You don't need a licence at the moment, even if you had one it won't change anything.
You might go to the Artsoft site and get:
Mach3 CNC Controller
Software Installation and
Configuration
Manuals seem to work best when read, sometimes more than once.
Craig