I have a very similar routine as Shinysideup. Basically, I interrupt the starting sequence with putting on gear, so the bike has time to do what it needs to do without interruption.
@Jeff: Thanks for the tip about the kill switch. I had the bike shutdown while on the highway, and had to pull over to restart the bike. Lucky for me I was on the rightmost lane, and didn't have to cross lanes of traffic. If I can simply cycle the kill switch and then press the starter, that would be much safer (although I suppose you would need to keep off the throttle while doing so to avoid the S65 error).
A follow up on the B9 error.
I just got the official Empulse Manual (it has the torque values for the oil drain plug! Yay!). Like the provisional manual, it does not list the B9 error.
After letting the bike sit in my garage over the weekend, the B9 error miraculously went away. And after pressing the start button for long enough, the bike started up as well. (Not sure why but sometimes it take more than the prescribed "3 seconds" to start up the bike. This time it took about 10 to 15 seconds.)
The bike appears to be working normally again, but I would rather not have to rely on prayer to get started, so I sent more logs over to Brammo. I hope that they can figure out what happened. For the moment, I haven't heard back from them, so either they're stumped, or very busy.
My guess is that the heavy Florida rain is taking it's toll on the poor bike, since I've had a few things go wrong during, or soon after, an hour of tropical downpour.