The transmitter is mounted to the inner fairing on the lower left (clutch) side. You have to remove the outer fairing, then it is obvious. Unlike when you buy a kit and install it yourself, this one was wired by H-D and has a real connector from the bike harness. Once you have the outer fairing off, you should be able to trace the wires from the transmitter back to where they enter the interconnect harness. The power wire goes to the cigar lighter (see attached drawing), the other wires go back to the connector at the interconnect harness.
The only way I can imagine the HID install screwing up the GDO operation is if you had to splice wires into the harness for the HID kit and you managed to do so in a way that cut power to the transmitter or isolated the wires for the headlight from the transmitter. Once you have the outer fairing removed, you can verify the transmitter is operating by cycling the high beam switch with the bike powered up while observing the LED on the transmitter. If the LED doesn't illuminate for a second when you go from high to low to high or vice versa, you need to check for power on the wire coming from the cigar lighter. If you have power, then you will need to check the wires from the low and high beam circuits to make sure any splice didn't eliminate those connections to the transmitter.
I wish I could be more precise, but with mine stored under a cover out in a freezing garage, and the manual being less than helpful, I'm rather limited.
Jerry