I'll look into an external regulator. Sounds like a good way to handle the alternator.
Both the solar controler and charge have battery temp cables and over temp protection.
We are putting a 135 watt on the dodger and two more on the bimini when we get it done (in progress) and one other like a 135 or 80 on the bimin for a total of 4 (3 on bimini). Not sure of the last size on the bimini. It will depend on if we decide on a window in the bimini. Four 135 watt panels will about fill the controller capacity. So if we move the boom over the sun should stay on the dodger top. Also I was told if you hook up the panels in a series they are a bit less efficient but if one is shaded the rest still work fine and most of the shaded one also.