For those looking for a solution for charging 24v/36v battery banks I think I've come across a really excellent product.
Minn Kota 2/3 bank alternator charges.
http://store.minnkotamotors.com/prod...C_%283_bank%29
These are designed to charge battery banks for electric trolling motors and can balance charge the batteries in series from a 12v source without needing to break the series connection between them.
It looks to be an excellent solution and they can be found for $106 for the two bank (24V) or $138 for the 3 bank (36v) version on Amazon.