"The thinner wire is definitely one of my concerns, it's gotta run from the left side of the bus underneath the body all the way up to floor level on the right side underneath a cabinet, which is at least 9 or 10 feet once all said and done. It doesn't have to charge terribly fast though."
The wire size does not control the rate at which the battery is charged. The state of the battery and the regulator in the alternator determine the charge current. If it decides that the battery needs 60 amps for example, it's gonna try to supply it no matter the wire size. In that case, anything less than #6 will just melt down.
This is just an example, but you get the point. Put in the biggest wire you can. Some things you just can't go cheap with.
