The output of the alternator assumes "ideal conditions". When the boat builder bought the engine it came complete with an automotive alternator. That is, this is the same alternator with in-built regulator that is in your car. In a car, it is fitted beside the battery, with short cable runs, at the same temperature as the battery and was only ever intended to top up the battery after starting the engine and run a few lights, radio, heated rear screen and so on. It was never intended to re-charge deeply discharged deep cycle batteries, and in its standard form, it cannot. Typically, the output from an alternator with the engine at 2000RPM will be about 30 Amps. This is because the internal regulator is "machine sensed", that is, the regulator controls the output of the alternator with reference to the voltage on the output terminal of the alterator. In a car, this is fine, as this voltage is almost the same as the voltage at the battery terminal, in a boat, it is never the same, due to longer cable runs, undersized cables and high temperatures in the engine compartment. The regulator needs to sense the voltage at the batteries not at the alternator.
Even if the regulator could sense the voltage at the batteries, it would still only be a fixed voltage battery charger. Fixed voltage battery chargers attempt to maintain the voltage at 14.4 volts, which is sufficient for charging a car battery. Deep cycle batteries need three-stage charging, bulk, absorption and float. The first two stages are the most important when charging over a short engine run period, such as when blue water cruising.
This means that the engine will need to be run for more than 4 hours per day to recharge the batteries. On most boats, this is bad, it means running the engine at fast idle, with no load on it. This damages large diesel engines, it is not what they are designed to do.
There are two ways to overcome this problem, fit an external regulator to control the existing alternator or fit a larger alternator with an external regulator.
An external regulator monitors what is happening with the voltages at the batteries, rather than what is happening at the alternator. It also changes the alternator from a simple charging device to a three stage battery charger, that is, bulk, absorption and float stages. This is the only way to properly and fully charge deep cycle batteries. It is important that this regulator can also sense the battery temperature. Cold batteries require a higher voltage than warm ones to charge properly, warm batteries require a lower charging voltage to prevent gassing.
Replacing the existing alternator with a marine alternator and external regulator is the best route to go, particularly if the condition of the original alternator is suspect or unknown. The Balmar marine alternator is probably the best there is.
"Charging from the mains to follow."