Dave, I'm not suggesting the batteries are deader than a doornail or have a bad cell, just that significant capacity has been lost due to inadequate charging. Thin Plate Pure Lead (TPPL) batteries are AGMs and it is well known that AGMs suffer when inadequately charged and/or left in a Partial State of Charge (PSOC). TPPL batteries have been around a long time and are extremely popular for uninterrupted power supplies necessary in the telecommunications industry because they have a large capacity and can be recharged quickly, some as high as 1C, i.e., a 100 ah TPPL Battery could be recharged in an hour with a 100 amp charger.
According to Odyssey battery specs the minimum recommended charge current is about 15 a. In the OPs installation, the charge current is roughly ⅔ of the recommended charge current. Alternator charging is not much better. Since the charger is really old, I doubt the alternator has been upgraded from stock, so we know that it is not up to the task of properly charging a high capacity battery. Even if the alternator was capable of providing 40a over a long period of time, it would still take 5 hours of motoring to go from 50% SOC to near 100% SOC. Charging from shore power is worse. Assuming 100% charging efficiency (a bold assumption) it would take over 8 hours to bring the SOC to 100% from 50%
For the sake of the OP's wallet, I'd like to be wrong. Those batteries set him back at least $1500, but the evidence isn't sending me down the failed electronics path. The definitive test for the batteries is a 20 hour capacity test, given the cost of the batteries (not to mention the chiropractor fees after moving them) the cost for a capacity test would be money well spent. I certainly wouldn't throw out $1500 worth of batteries because some guy on the internet said they were bad.