Just to clear things up a bit - I have another board that will be driving X axis and the extruders. There is no X configuration because I haven't finished building the machine yet, haha.
Glad to hear about the ability to home the axis without breaking the drives up! I'll update the firmware and programs tonight to see if it has any effect on my problem. Thank you for the tip!
Infinite improbability drive, hahaha! Definitely going to use that as an explanation in the machine shop tomorrow!