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Maybe a bad alternator fried the batteries - who knows. Your truck, your call. Maybe cleaning the terminals and grounds helped. We can't tell if you don't post it.
btw - Optima batteries are not what they used to be and IMO there are better choices.
Maybe someone else can think of another reason for everything working with a jump from another battery (or batteries), but nothing with just your trucks batteries.
No, there are three redundant grounds per se that can power the initial electronics, the 8ga at the pass battery, and the two 12ga as bonding cables. Even if one of the ground cables off the batteries was disconnected, it would still have one. Maybe one completely dead battery and a bad cable combination(s). Time to start asking for pictures of the battery connection and more.
I'm not sure that the percentage off the charger is telling the charge level, it makes no sense since the batteries were drained to the point he mentioned.
As you said, first test the batteries with a real tester, install, measure the voltage at each point when reconnected.
Edit - and where the jumper connections were placed.
i guess i will give that a shot first before buying a ficm
Its a big leap to think your issues are in the FICM. With the proper scan tool you can do some diagnostics like FICM voltages, sync, codes etc. You can have a FICM tested too.
Get ahold of the Forscan app and obd2 adapter. Then when folks ask for some sensor outputs it becomes much easier and hopefully less expensive to get it back running.
So i replaced the fuel pump, new alternator, and had the batteries charged at a battery supply store. Primed it several times, it started, rough idle at first then leveled out. Let it warm up, shut it off, tried to restart it and nothing. Just crank crank crank.
hooked up an obd2 reader, harbor freight, and it said codes found 0. What reader should i get or does anyone know anything that could point me in the right direction?