Let me start off by saying I in no way really know what I'm talking about as facts. I'm just speaking from experience I have seen.
1) I don't think the voltage is as important as the amps being pushed.
2)To clarify what I was seeing was that after a three + hour ride home I connected the charger and according to the LED indicators the battery was not recharging. I do leave the charger hooked up overnight in my garage to fully charge the battery.
3)I agree the CTEK probably doesn't produce enough juice to be considered a High-output charger. I referenced the manual to show that it states to disconnect. I would rather be safe than sorry when dealing with a higher priced piece of equipment like a refrigerator.
4)My understanding, I could be wrong, is that our 5th gen trucks have a system that regulates the alternator to a point that if the system believes the battery is fully charged it reduces the output of the alternator. Therefore not producing the amps needed to charge an AGM deep cycle battery fully. No matter how much time you spend running the alternator.
5) That's what I was stating. In order to fully charge the battery fully it needs to be hooked up to a charger. In my case I have one battery. Like the OP I'm using it as my starter also.
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1) Voltage is very important, it's the way the charge actually works, the current is simply the amount of energy that could be put through the wire or is put through the wire. Voltage and resistance will determine how much current flows. When your battery is low, it's voltage is low and the battery will charge because the voltage differential of the charging system is higher than the battery voltage, as the battery get's charged up, it's voltage rises, and eventually the charge will slow and stop. Amp's are never pushed, it's the load(discharged battery) that requests the amps/current from the source. The load will request as much as it needs, it's then up to the system to be able to supply what the load wants. If the battery is low, and you have a hundred amps to throw at it, it will accept the 100amps, if the charger is only 7amp then the max the battery will get is 7amps.
2) sounds like your battery was charged as much as it could be at that point with the stock charging system.
3) yes, its not a high output charger, a high output charger can actually jump start your car from it's charge(like the big ones they roll out at the auto shop)
4) yes, the alternator/voltage regulator is not made for AGM batteries so you will never get full charge simply because the voltage will not go to 14.8.
So, for me, I don't know if installing a AGM as the main is the best idea here, but if the voltage boosters work out properly, then it should work fine I suppose.