Thanks for the details. They help a lot.
I have just 3 observations:
1. Check especially the fuse connections -- the 200A fuse (I assume it's an MRBF since you said it was on the battery terminal) and the inline fuse on the battery sense wire. These can develop surface corrosion
which you can't even see.
2. The charging amperages from the alternator seem about right.
3. I would NOT trust the battery monitor to tell you when the batteries were "fully charged". They are notoriously unreliable unless frequently calibrated.
How to tell when they're "fully charged"? Put them on a good battery charger
(like the Sterling) for at least 24 hours.
It takes quite a few hours to reach "full charge", even with a big charger
Your 50A Sterling charger at full output represents only about 7.6% of the capacity of your 660AH AGM battery bank, and that's without taking account of other loads which may be present.
Here's what a 10% charger looks like on Concorde Lifeline AGMs during the first couple of hours charging a 50% depleted battery (the blue line):
And here's the percentage of CA accepted using different size chargers...sorry I don't have a 10% charger figure, but you get the idea.
As to CAPACITY remaining in those AGMs, the only way to tell for sure is to do a controlled load test, preferably with a fixed C/20 load over a 20-hour period. Failing that, a good capacitance/inductance tester like the Midtronics series will give a decent approximation. See if you can borrow one.