What I would like to do is modify the sketch to "look for" a csv or txt file when powered up and read that file to create the firing commands for the controller, so the system can be used with a computer and the firing software OR the text file on a portable storage device.
There are examples of reading text from a SD card in the SD library. You should be able to modify the example to deal with the fact that the file might not be present.
I am also figuring I would need a "trigger" of some sort to start the file program (ie press button to start, press again to pause/stop, press again to start from pause/stop point
OK.
when connected to a computer and with the software connected and running it would ignore csv commands, does that make any sense?
What software? Detecting that the Arduino is/is not connected to a PC is not a trivial task. Without the PCs knowledge/active support, it is, in fact, impossible.