I think you need to change your Ports & Pins Motor Outputs to:
X step 2
X dir 3
Y step 4
Y dir 5
Z step 6
Z dir 7
A step 8
A dir 9
Follow the wires and check which pin your EStop is connected to and make sure that is the pin specified in Inputs for EStop.
(The 3163B diagrams show pin 15 but yours may be connected differently).
Check JP2 (as mentioned previously).
Tweakie.