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Just to make sure I understand, you connect a scan tool, and the car will crank, start, and run fine?
Most likely there is something on the data communication circuit that is pulling the power from it and this is causing module communication issues, and the scan tool is allowing the circuit to power up. When the scan tool is connected are you getting any U codes? Can you communicate with all modules?
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Back probe the data link connector green black and white wires. See what voltage they have with the key on. Then plug in your scan tool, does the voltage on these wires change?
I do not believe running with the HUD plugged in is going to hurt a thing.
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