Thanks for the advice, All.
I found a long advrider post this morning asking my exact question, and the replies were all "disconnect the battery, get a good ground, leave the electronics connected, never had a problem" so I was not too worried.
I ended up disconnecting the battery and the ECU under the seat. Now I need to paint the bare metal.
Shock adjustment ring is a little harder to get to, but it's not a big deal.