Oh I understand that completely. My current design has an FTDI to act as the USB to Serial for updates from the Arduino IDE. I'll be burning the bootloader to the final product to make it work.
Now, since the gun unit normally will be running on a power supply seperate from the power provided from the usb cable while its in operation in the gun, would I be able to use that as a trigger/condition as to how it talks to the unit, getting the avr to connect the pull ups for TWI when connected to the external pack, and cutting them off when not so that the pull ups wouldn't affect the USB lines?
This is how I think I could set this up if I were to stay with USB: