you're overthinking things.... sounds like your voltage regulator is slow reacting. normal caps usually need a very high, like 16-20farad to make up for this, but supercaps just work diffently, and they should fill-in that surge. they arent going to charge up like you think. they are going to stay at battery voltage, then a slight bump in power to reach alternator volatage, but not like a huge short circuit type of event. the second battery is going to tax the alternator far more than the caps will.