To reverse the BLDC you need to given there are three phases U,V and W, and hall sensor signals A,B and C you need to swap the wires U and V, and the hall sensor wires A and B.
This is assuming A and B are the sensors for the U and V phases.
Start spindle at the slowest speed in manual and see if it runs.
If not restore to original and try a new combination.
With a BLDC you must swap the motor wires and the hall sensor wires that belong to the swapped phases.
If you get it wrong the spindle wont spin and will get stuck when turned on.
It is best to read the Motorola notes on the MC33033/ MC33035 family to get an understanding of the operation.
You need to set soft limits. Works fine once set up correctly.
Follow Mach3 manual.
The E-stop is just that. For emergencies. Don't rely on it for the limits.
The machine has no safety relay, so the E-S operation is somewhat poor.