M03 Sub Routine File Location

Currently working on a machine using the QTPlasmaC GUI, and I was wondering if there was any way to access the M03 sub routine file anywhere? I would like to edit it to disable the homing of the Z-axis that it does. 

Right now the machine fires the torch using a regular output pin, which works fine when everything is going perfectly, but when a limit is triggered or the E-stop is pressed, it doesn't quite understand that it needs to disable the torch as well. 

I was able to almost work around this by messing with the hal file and using an and function to turn off the the torch when the e-stop is pressed, but the problem is when the machine is reset it has a memory of last being told to turn on, and so the torch fires.

My thinking is that if I can go in and mess with the M03 instructions I can just completely disable the Z-homing because all of this has been a work around for that, because my machine has no z-axis. 

Thanks!

I may not be asking the right question. Is there a way to ensure that when the estop is pressed or a limit switch is triggered, to tell the torch to come off and not come back on?

I thought maybe by editing the M3 g-code, I could get it to work for my machine and also get the estop and limits to turn off the torch.

Is there any way to link the output pin 00 to the estop and limits, in such a way that it wont turn back on even when the machine is reset, and stay off until it gets a new command to turn on?

My next idea is to make my own M code that has my needs in it, but i feel that i will still run into the same issues where the estop either doesnt turn off the torch, or if it does, the machine "remembers" it was firing and immediately arc.