A 100-amp alternator with a good external regulator (like the Balmar MC-612) would certainly be an improvement.
There's no issue of conflict between the external regulator for the alternator and an inverter/charger. The charger
part of the inverter
only works when you're plugged into shore power or an onboard generator
. It then takes the incoming AC, converts it to DC, and charges the batteries. Providing, of course, that the switch labeled "inverter on" in the diagram isn't open, in which case there'd be no charging
going on and no inverting either if I understand the diagram correctly.
It appears that the alternator is now connected to an isolator, thence to house battery
bank and to the start battery. A far better arrangement would be to lose the isolator, connect the alternator output directly to the house battery bank -- with an appropriate fuse near the batteries -- and to use an EchoCharge or DuoCharge to keep the start battery topped up. This is more efficient and, once properly installed, requires no further action on your part.
IMHO, the marine
electrician is still a very good idea. Could save you lots of $$ and heartaches down the line.