Do you have jogging control over the Z axis when in manual mode? This must work first!
Review all the notes in the thc-toma-stepper-final package. Make sure that your values make sense for an imperial units system. Pay particular attention to the signs of the parameters you enter. The switch offset (SwitchTravel) and pierce gap (PierceGap) both can cause big problems if the signs are wrong! Slow your Z axis response way down for openners, use a velocity of .1 ips and an acceleration of 5ips^2(these must be changed for both the axis and joint in the .ini), you can set it back to the correct range you established during your initial calibration after the motion is correct.
Manually create a simple Gcode file to test with. Just a single cut, either a straight line (6" to 8" long) or a rectangle. You will need the single straight line file for speed/voltage testing later anyways. Copy the format Tommy used in the cncbytoma.ngc file ( this file appears to have been generated by Gcodetools), this is in the thc-toma package, your file will have only one cut and only be a few lines long. Post the file here so we can see what is supposed to happen. A detailed description or video of any problems using the simple file will help the group figure out what may be wrong. Also single stepping the program will help determine which action is the problem.
John