It's done! Well, almost.
I received the replacement bulbs yesterday and after some finagling, got all the lights working. It turns out, I had wired the rear light backward, so the brighter light meant for braking was always on. The contacts for front right turn signal bulb were also rusted over and covered in some mysterious white powder. In addition to all of this, the horn just wouldn't work for whatever reason. I spent 20 or so minutes trying to diagnose the horn: it worked when connected directly to the 6V supply, there was no grounding problem, and the two spade terminals showed 6V. I think that somehow the horn isn't getting enough current, although it starts to make noise at 3A. I eventually called it a night.
Today, the boost converters came in the mail and as soon as classes were over, I wired the converter in. It's grounded to the frame through the engine start switch, and gets 6v from the wire leading to flasher. The idea was that I would be able to kill the controller logic power using either the key switch or just by switching the engine start switch to on (no it's not opposite day). For whatever reason, this didn't work during testing - something that I should probably figure out for the sake of safety.
Ignoring both of these issues, I decided to go for a test ride anyway. But before that, I let a couple people on hall ride it up and down the hallway. One misjudged the amount of torque it had, and the Yamahopper promptly flew out from under him, smashing the taillight. Whoops.
I went for a ride anyway, putting about 8 miles on it before returning to EC. It handled it like a champ, easily hitting 30 mph (48 kmh for you Canadians) with the throttle wide open. I was able to pop a couple of wheelies while accelerating down Amherst Alley and the Esplanade. Despite a label telling me not to take passengers, I took a friend from Building 24 across the Harvard Bridge and back, and finally to their dorm. However, there wasn't a whole lot of clearance between the rear wheel and the battery enclosure, as the suspension was pretty soft. In addition to this, the suspension was also probably close to being bottomed out, which made bumps a lot worse.
I'll have to fix these last couple of problems before I start using the Yamahopper at night, but I can't envision myself doing that in the cold and snowy Boston winter. It's at a state where I feel comfortable driving it around during the day for groceries and stuff like that. It's almost done, and until something goes wrong, almost is enough.