I've been using the G540 XML but now that I've bought a THC301D it is provided with a new XML.....which one do I use, are there G540 specific changes that I need to make within Mach 3 if I use the new XML for the torch height control?  I havent installed the THC yet, I just wanted to be ahead of the game if I had problems.

I think what I need to know is wether I can combine the two profiles without having to manualy set up my ports and pins.

No, you will have to enter the values specific to your machine if the xml you are loading is different.
Hood