Hoyden,
Lots of good info here... but I bet it is starting to feel like "too much!" for a self-confessed electrophobe!
So, let me try and glean some of the key points for you:
1) Your solar panels are probably fine
2) Your solar controller is crap by design
3) Your batteries have been stressed by repeated low charge states and insufficient charging, but will probably be fine if you fix the charging problem
4) Your truck charging system will not do a good job of charging your camper batteries without some major changes
Details:
1) You confirmed the wiring, and the 22v at the controller is good. You could do the current test that Happyjax suggested, but I do't think this is the issue
2) This is the issue as Apointed out. 2 hours is NOT enough for bulk/absorb charging. I can explain why, but for now this item just needs replacing. I like the Victron gear. Trimetric works well too. Get BOTH the charger and the monitor, regardless of which of those two you get. Part numbers to follow if you want them. Oh and don't worry about that extra set of terminals on the existing controller. Those are for a second set of batteries if you have them, as per your manual
https://www.outsidesupply.com/dual-30-amp-pwm-solar-charge-controller/
3) Batteries don't like being stressed so much, but are pretty tough. In the grand scheme of things you didn't hurt them much. IF they had frozen while this discharged, that would be a different story
4) Like you said "From that video, what I could gleen is that stock alternators often aren't up for the job of dealing with all the new stuff" This is true, especially since you drive a Toyota as pvstoy said. A burlier Toyota alternator will not make a difference. Toyota uses a charging profile that puts out a fairly low voltage to the truck battery, meaning that by the time that juice gets to the camper it won't have enough oomph to charge your camper batteries.
Other bits...
A) Your batteries are not huge. 2 x 79AH = 160AH or so. These are yours -
https://www.batteriesplus.com/productdetails/sli24magmdc
Plus which the batteries are not true "Deep Cycle" batteries like a golf-cart battery would be, for example. No biggy now, since you have them already. Just be aware that any battery that lists "starting" in its list of applications isn't designed optimally for running your camper.
You asked if the "Blue Sea unit I have in my 2016 Fleet provide the type of modulation of current from the alterrnator that my 75 aH AGM battery WILL accept?"
- Yes, and no. Your alternator could charge the batteries in your camper if the wires going to it were thick enough, and if the separator didn't disconnect too soon. For Toyotas, the CTEK 250 is a good solution, as it bumps up the voltage nicely. Bernard on this forum uses one. But FAT wires are a good start. More details when you want them
C) Bill/Advmoto18 is right on the mark. IF you want to charge from the alternator/truck while driving... and I say IF... because if your solar controller was working right you would rarely need to charge from the truck. I have built my camper/truck to charge from both sources, and my alternator puts out BIG amps (80A is the highest I have seen) into my camper batteries
D) Should your solar panels be able to recharge your batteries? Maybe. You have 160AH total. 50% is 80AH, which should be able to run your fridge for at least 20 hours continuously. At which point the volt meter should read somewhere around 12.2v. You are not getting that from your batteries, (except maybe on the first night after being plugged into shore power for a while?). If your solar panels are 160W like the latest FWC are, then you generate ABOUT 50% to 80% of that most of the time. So you should see about 8-10A from the solar panels going into your batteries. If they are at 50%, you need 8 hours of continuous sunlight to get 80AH. Make sense? So your system is sized about perfectly to recharge your batteries every day, IFFFFF you get good sun for 8 hours. Anything less than that, and you will not recharge fully. Do you see now why your controller is junk? It is designed to give only 2 hours a day. Hopeless insufficient.
E) I see you added a measurement... 5A. So now you need 16 hours of daylight on those panels....
F) Maybe you do need BOTH a better controller and monitor, AND to beef up the charging system.
Phew... ask more questions!