Um..... If you read you would realize that there is no Pi in my setup as it stands right now. I only printed the case for my Pi 2B+ last night and haven't plugged it into the printer yet. I built my own power supply for the Pi with dual 7805 linear regulators (one is clipped off until I install a diode for it, lazy/not critical yet, heat ok) and I've tested it with 12v 2.5A input and finally don't get low voltage icon like trying to run it from a 2.4A USB charger. It will be pulling 24v from the printer's power supply so I imagine it will remain just as stable.
This issue has actually been solved and was found to be Cura taking over the port upon printer reconnection. Thank you though for stopping to help. 