OK there are several things to change or check.
Motor Outputs:
1) you have the spindle enabled with its step and dir pin set to pin2 of port zero. I suggest you disable this for now. We can sort your spindle later.
Input Signals:
1) Do you actually have limit switches on your machine? if YES then OK else disable the limits.
2) You have the E-Stop Emulated. Untick Emulated. If this solves the E-Stop problem OK else untick active low.
3) You have OEM Trig #1 set to the same pin as E-Stop. Disable OEM Trig #1
Output Signals:
1) You have the charge pump set to port 1 pin 1. Does your system need this?
Ian