I'm adding code to the firmware to have data be request instead of being push from the ArduIMU v3. I have tried many thing to set up the handshake but none work.
So my question is: Does multiplexing the GPS off serial0 prevent the ArduIMU from receiving data from another micro controller (in this case an UNO)?
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I do not recall using a V3, but based on how the older IMUs worked, try this:
Pull D7 low to listen to the "A" input (GPS) of the mux.
Pull D7 high to listen to the "B" input (serial line on connector) of the mux.