Well I'd say it 's time for an update. I mentioned in an earlier comment that I was distrubed by the diving board-type of effect I was getting with my rear rack mounting of the capacitor and controller, not to mention that it wasn't the most secure setup if I parked the bike and walked away from it. After trying to make a secure sheet metal shell around the rack that was lockable and had rear access (which also scared me since the sheet metal was close to the cap leads

), I finally took Dennis' advice from his first comment in this thread and mounted everything in a trailer! I decided on a two-tire trailer for a bit more side-to-side stability. Here's a picture that shows the bike against a beautiful backdrop of junk in the lab where I've been working all this time. It was clean back in December...
Here's a better look at the front end. All of the controls are still in place, brake twist throttle, brake button switch, CA, thumb throttle from L to R. I cleaned up the wiring a good bit and waterproofed what I could.
And here's the back end. I put a large black plasitc tube to cover the trailer arm, and hid the three wires under it (motor phase power (3 conductors, AWG14), hall sensors (5 conductors, AWG18), and control wire (12 conductors, AWG22)].
Now for a look under the trailer cover. I have a large waterproof "Fibox" (made of tough plastic) with a lockable cover. It holds most of the wire mess and the cap, controller, shunt resistor, and a terminal block. I can see through the cover when it's locked to check the controller for any error signals (LED-based) without unlocking it. The Fibox is mounted directly onto the plastic trailer bottom.
A clearer view inside the Fibox with the cover unlocked and raised. You can see the gasketing edge around the outside of the lid's groove and also the switch I can use to power both the controller and Cycle Analyst on and off. With both of them off, the capacitor stays nice and charged - holds its voltage level very well overnight. Also in this configuration, I have easy access to the programming port (serial) on the Kelly Controller.
The terminal block is hidden behind the capacitor on the left. Here's a peek at it:
It's kind of a monster, 20 terminals with 0.44" spacing. I hope to not be playing around with it much at all. It took too long to figure out where to wire everything in the first place!
I guess the best part is that everything is detachable. At the place where the trailer connects to the rear hub hitch, I have plugs for all 5 of my device sets: brake wiring assembly (switch and twist brake), hall sensors, motor phases, throttle, and Cycle Analyst; I can unplug them all and take off the trailer and just ride the bike like I used to.
There IS room in this trailer for more stuff if I don't use the Fibox. Connecting three 48 V caps in parallel is not out of the question, nor is adding a 48 V battery for parallel connection with a single cap module. Riding with the trailer is taking some getting used to; you can kind of feel it push and pull at you when you are accelerating or decelerating, or taking a curve.
The weather has got to warm up soon, then we can take to the streets with some students and get some better data. I hope I'll have some Cycle Analyst-based data acquisition by then... logging V, A, and speed is going to be a must for my reports. Thanks to all here for helping this project along - especially Dennis for pointing me to the NineContinent motor (which has been great despite spinout issues), Paul and Miles for discussions on regen, and methods for some very critical assistance with the Kelly Controller.