1. Stepper motors do not typically "burn out". They don't have enough torque so when they get jammed the just stall. You can test the motor by measuring the resistance from the case to any winding. it should be open. measure the DC coil resistance. It should be close to the same (low ohms) for each side.
2. If the Gecko blows fuses with no motor attached it's a dead soldier. If you got the drive from us send it back and we will get it fixed.
Which of our systems did you get? Was it with motors, with geckos (full packaged system) or a bare bones setup.
It's hard to blow a Gecko from stalling the motor if the current is set right. With that being said we have switched to selling only the 203 drive in stepper packages.
Drop me a line and we can help you get things fixed and running again.
Limits on Z down are real hard to do. When cutting with the THC there is a soft limit if possible down Z excursion.
If you had the floating head in place how did you get it that far down? It will absorb several inches of Z "mistake".