I gues you should seek out the current alternator
regualtors as well as shore chargers both. You reeally need both. It also seems you ned both 24 volt and 12 volt wiring
systems as well.
50 amps is usually 220 volts on a shore connection in the US. Twin 30 amp connections might also be desireable too. It just depends on the overall wiring
plan. You'll be hard pressed to find newer shore chargers that don't have smart regulation but it is nice to have the ability to divide into multiple banks so you may choose a charger
than can deal with say 3 banks. These are quite common. You may also want to consider AGM
batteries since they stand on end without concern. They operate with any orientation so you can pack them as you will. It's just a matter of securing them so they can't fly around.
The USCG does not let cutters go until they are really beat. Best of luck getting it back to life. If you need more references
send me a Private Mail and I'll send you a link to a marina that does a lot of contract
work for the USCG. They may be able to give you details about the boats you might not otherwise be able to get.