If you aren't planning to run a 24V battery bank, then it might be worth your time to replace that alternator with a second 12V alternator for your house batteries. To offset that cost, you could then sell your (tested to be good) 24/28V alternator to someone wanting to run a 24V battery bank, like me!
I would have reservations about running circuits tied to a single battery in a series pack. I personally feel it is better to have a single common ground on the entire vehicle, and doing it that way would mean divorcing the DC circuits from the chassis ground entirely.
Don't forget the KISS principle.