Wrong, Wrong, Wrong. If the 'local repair shop' did indeed leave you without a way to reacharge your house bank away from shore power....then they should never ever get another job from you again.
What you did right:
1. Increased the size of your house bank to meet your needs.
2. Felt something was amiss with the 'repair' and came to Sailnet to confirm.
What you (they) did wrong:
1. Leave you without a way to charge your house bank.
2. Didn't fully understand the problem (as you describe, charging takes longer than you'd like/prefer, etc)
It is fully acceptable to create 2 separate house banks, plus a third 'bank' for the starting battery.
That said, the most commonly recommended setup is one large house bank, plus the starting battery. These banks are completely isolated from each other. Normally, the alternator output is directed to the house bank, with a paralleling relay or echocharger rigged in to charge the start battery.
I completely disagree that a larger alternator cannot be swapped in as a direct replacement for the OEM unit. With a 720AH bank and lead acid batteries, you can put in 25% of total AH capacity, or in this case 180 amp alternator. But, you wont be able to drive that big of a load with the auxillary in your Hunter....I'm guessing 100 amp alternator max.
Now, let's get realistic...I'm not sure if you're willing to spend the $$$ to reverse the work that's already been done. You should, but I've always like to spend other people's money :-).
At a minimum, you should have the output of the alternator moved back to the house bank.
You should consider combining the (2) 360 AH banks together, but this is not 100% necessary and since all 4 batts were not replaced as as set...
Add a paralleling relay or echo charge from the house to the start bank.
If you want to break the bank....replace all 4 house batteries with AGM type batts, these will suck up all the current your alternator can thow at them. This will ultimately solve your initial problem of 'it takes too long to charge'
Replace the OEM with a drop in replacement P-type (externally regulated) alternator up-rated to 100 or so amps.
Can anyone tell I haven't had my coffee yet....I am a little wordy in the AM.