RnRMotionController will not recognize any limit inputs or estop. any ideas as to why?

If you are not able to get any indication that an input is working, make sure to set the port of the input to 3 and set the pin of the input to the input number on the board. If you are using proximity switches, make sure you are using an NPN type and you are setting the active low toggle depending on if the switch is set for normally open or normally closed operation. You will also want to make sure the switch is wired correctly for either normally open (in parallel, like a ladder), or normally closed (in series) and make sure the correct leads are used on the switch.