well given that E is your extruder control of out feed goop, it will be set to some constant rate for the feed you have set. To convert the E to some other axis, i.e. C like in your example, I suspect you would need to parse the Gcode file in a plugin, find all the "Exx.x" and convert it the repost it to the G code window. kind of a pain in the butt, but do-able. Your other option is to do a Find-Replace operation in a text editor, switching all Exx.x to Cxx.x in the file, then save and load it in mach3.
Since you have a "Warm up time", I would Edit/make the macros you speak of for a pause time for warm up time that could be pulled off a "User DRO" on your screen. Your spindle in your case sets a temp, that implies some type of "Warmer/Heater" system that takes some value to set its temp. So, I would assume, that that spindle value in your current machine, would be some kind of "Digital value" like a 8, 10, or 12 bit value, if that is the case, and your heater is on Modbus, you could send it over modbus. If your heater takes an Analog 0-10v control value, you could also send it out as modbus to a "interface device", like: Peter Holmans ModIO, Aurturo Duncans Modus boards, or a ADC PLC like an 05 with an Analog module in it.
Further, if possible, the CAM that writes your current machine extruder programs, I would see if you can Edit the post Processor to change the output type to what mach likes, THAT would be a Great Option.
scott