Didn't read through everything, but I can tell you a few problems to begin with.
If your batteries are only resting at 12.6V then they are either bad or you are not getting them fully charged. A 12V battery is fully charged at 12.9V with optimal charge voltage of 14.4V. If your connections are good and your ground it good, then you should see the same voltage at your alternator, your front battery, and your back battery. Your amp should be getting the same power as your back battery, or within a tenth or so.
Best way to test the batteries is either take them to an auto parts store and have them hook the batteries up to the Midtronics tester (takes about 1min to test them), or pull them out and fully charge them with a good charger. A fully charged 12V battery just off the charger should be around 14.4V and after sitting for about 12 to 24 hours it should be resting at around the 12.9-13.2V range. If the battery drops down to the low 12 to high 11V range then you have at least one bad cell in the battery.
AH has NOTHING to do with batteries when it comes to car audio applications. AH ratings are low amperage pulls for extended periods of time. Car audio has high amperage pulls for short periods of times. So, unless you are using the battery to run a 10amp light for 20hours the AH means nothing.