The dealer north of Milwaukee came down to the Chicago 'burbs and did Travelin's and my bike today in my garage. It was kinda fun watching them do the work. The changed out my VCU, and did the rest of the update. Travelin's was just the firmware upgrade. What was cool is he logged into my Wi-Fi, and then called Brammo to have them remote in to check the work to make sure everything was done correctly. Quite impressive.
A few notes: my fuses were already the "updated" values, but Travelin's were the higher capacities. So sometime right before my bike they switched over.
They re-tapped the connector under the cowl, and also tapped a long many-pin connector right above the radiator. I am thinking that the long many-pin connector was causing my problem, and not the VCU. Instead of Gaffer tape they used "amalgamating" tape. I'll be out cruising tomorrow to see if I notice any difference.