It certainly sounds like a very interesting project that you have undertaken.
If you have the time it would be nice if you could start a new topic on your Emco machines with some pictures and more detailed descriptions / explanations on how you have made everything work with Mach3.
Mach3 just works on the Gcode that you give it. The excess Z axis movement which you describe is presumably being put into the Gcode which you have created from your Q-Cad drawing ? If that is so then this is the area in which you should be looking. See if you have a Mach3 friendly, Q-Cad (or whatever you are using to create the Gcode) post-processor, intended for Plasma.
I no longer have an X4 to check the spindle set-up for direction control – perhaps someone else can help with this (this thread is old so it may be best to start a new topic asking the question).
In Config. / Ports & Pins / Spindle Setup you can specify a ‘Spin-Up Delay’ – Gcode execution is paused for this period of time to give your spindle time to get up to speed.