Well… i redid my torch fire wires to go through the cnc port and after a few choice words soldering the 1-2 pins to the wires it seems my alarm issue has gone away. I managed to cut a few parts out, probably 30-40 pierces and it has not happened again. So it seems that my issue with that is, at least for the moment, resolved.
The air triggering on and off after cutting is still happening but that will probably be a no post for another section. Thanks everyone for the help