Well today... another update...
A few weeks ago after activating the auxilary power system using the two behemoth batteries that provides 100 amps per hour... Mind you, I had a 95 amp alternator which is the stock in most F-150s in the 2004-2006 year range. A week ago, this alternator died. I was shocked that it died this early. Lucky for me, I took it in for warranty repair and they let me keep my dead alternator because I figured I might be able to rebuild it and use it for later.
Guess what? I find out quickly that the load that was put on this alternator was astronomical. I had three batteries that this alternator was supplying power to. I also have two amps totaling 1475 watts of power and at 14 volts, that is around 105 amps of total output capability. I rarely go up to 50% of this capability. Now, you can see how everything all added up. I was consistently taxing this 95 amp alternator.
I came across a site that provided extremely high output alternators in the same package as the OEM ones. They're just rebuilt with more wire windings and doubled number of diodes and rectifiers. The chassis of the alternator is the exact same as the stock one but does 105 amps at 850 RPMs and then jumps to 215 amps at 1200 rpms. I bought this alternator for 229 and got it last night and installed it myself.
My problems are now solved. Except that I need to do-away with the stock battery as the main battery. The back batteries are deep-cycle batteries and the main battery is just a regular ol' battery designed for more cranking power. So, I'm going to buy an Odyssey PC1700 battery to make all the battery technologies all the same so that way everything's all completely safe.