Here's a couple of ideas I was thinking of trying when I get around to putting caps on my Bug (I have to rebuild the engine first
).
First, why not hook the caps directly to the starter, but put some resistance between it and the alternator (and any battery). That way you get full power to your starter, but the caps don't put a strain on your alternator.
Also, why not have two resistances. One could be activated by a high power relay/contactor when you hit the brakes. This would be low resistance (or no resistance), and kind of work like a hybrid system, causing you to bog down your alternator, but only while stopping. The other route would be high resistance continuously (or no connection at all).
A head lamp or series of 12 or 6V incandescent lamps would likely work. The neat thing would be that it would offer more resistance when there's a high voltage difference since the lamps would heat up and cause more resistance. But as the voltage levels out they would heat up less and lose some of their resistance. The lamps would also allow you to charge your caps from 0V without effectively short circuiting your electrical system.
I do prefer the idea of using caps over lithium or lead acid, but because it gets very cold here. It's common to see temperatures as low as -40° F (-40° C). (Yes, that's forty degrees below zero
!)