Don,
I should have just called you. I'm sitting here with my bro-in-law and I told him "I should just call Twolane", now were laughing..... I just did a bunch of stuff to my 05SEEG and when it came back from the shop and the bike to reciever (Garage door) isn't working. Any thoughts??
If the pieces are all installed (or at least assumed to be so) here's what I'd do Matt:
1) Watch the LED on the receiver while operating the controls on the bike to see if it blinks. If it does not pull the fairing so you can check all the connections to the transmitter.
2) If the LED on the receiver does at least blink then unplug the receiver from the wall, plug it back in, hold down the button for 15 seconds or so to clear its memory then re-pair it with the transmitter.
Never being one to trust coincidences have to ask; what was the bike in the shop for? Anything requiring work inside the fairing or any electrical work whatsoever? We both know that if anything was done in these areas it is the most likely source of the problem.
Good luck getting it sorted Matt. You know you can feel free to call anytime

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