As a follow-up and closure... after a very long time of trying different fixes; I decided it was too costly to cut my losses and sell and purchase a new rig - so we did a complete top end rebuild.
Meaning, new heads (o-ringed), MAHL gaskets, ARP head Studs, FoMoCo rebuild fuel injectors, new Adrenalin HPOP, new coolant oil cooler, new FoMoCo injector wiring harness, rebuilt FICM, new FoMoCo IPC & IPR, 6.4 pushrods, upgraded 6.4 banjo bolts, new rear fuel crossover, new blue spring kit, upgraded egr delete, turbo clean, and replaced the old Edge Juice Attitude with the CTS3. There are probably a few other things I cannot remember which were checked, cleaned, replaced, or tweaked.
It now runs like new after all of the air left the system. This means I did not figure out the problems with my engine as I replaced about everything. This summer I will replace the turbo with a stage 1 'screamer' model. My latest challenge is to figure out what is the best programming to use on the CTS3 and purchase a fuel pressure sensor to add to the system.
The cost for parts and labor was probably around $7500, as I did hire out this job with a small local shop who could pull the cab (where I could not) and has more experience trouble shooting these things. I am very pleased with the way it runs and have 1000 miles on it now.
Also, there wasn't anything in my fuel tank as suggested to check for 'growth', just clean fuel. I use a coffee filter on an arm to swab around and looked at the pick up assembly for contamination.
Thanks to everyone who helped provide input with my vehicle challenges, I appreciate this forum and the people who feed it.
Ken (MuleMan/6BarJ), NW Wyo territory