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My truck has decided it is done with the transmission finally after almost 210k miles. Maybe?

Unless anyone has experienced what these issues might mean for the truck, little background here:
Bought in 2015 with 125k miles on it in Denver, CO. Got the 'extended' warranty, tried to cash in on it when started having overboost/vane sticking issues, was fought the whole way, never got the work done.

Moving on to 2016, towing out of Phoenix, AZ with a 10k lb 5th wheel, got mechanics light on dash after pulling up a hill just north of Phoenix, dumped the trailer on the side of the road, went in to town, took it to the Ford dealership and was told new turbo, $3k. Said, no, we're broke right now, even if we wanted to, would have to wait days for a new one to get there. Took it back and took our chances, did some research, turns out, turbo was fine, my EGR had been sticking and causing loss of boost pressure under acceleration. Went to AutoZone, replaced EGR=back on the road again.

Fast forward to 2017 beginning of year, back from two weeks overseas, get truck, drive it for few weeks and then it starts billowing white smoke on the highway, replaced EGR again, it does it again couple weeks later, tried replacing EGR, no go fix this time. Think it's the TCC solenoid based on research, have it towed to friends house, replace that solenoid, still nothing, appears to be a dead battery issues?? So another friend comes over with his 6.0, charges mine up and she's good to go. Get new batteries, new alternator, all is seemingly fine. Weird right?

Did some more research online, decide that it might be time to replace the FICM and do some of the 6.0 'PM' work necessary on the engine to work my way towards 'bulletproofing' this SOB.
- New FICM from Ed with the 'upgrade' tune of 150HP?
- New oil cooler
- Finally deleted EGR system, left EGR in place and plugged in
- Some new sensors
- The high pressure oil solenoid that sits below the turbo?? (Can't remember name of it at this time)
- Rebuilt the turbo with new vanes, ring, new oil supply solid pipe
- New harness for every FICM plug (old ones were cracked and didn't hold well)
- New coolant tank
- New alternator
- SCT tuner to keep EGR 'off' and monitor values
- Switched coolant to CAT ELC (did an extensive flush with the scale remover and restore chemicals)
= All this, she runs great, if a little rough on the 3-5 shift that started happening

Fast forward to this year 2019, moved to Wyoming on way to Casper, get off highway, notice excessive amount of smoke while slowing down off the highway out of the tailpipe, head to buddy's place and continues to belch black smoke while accelerating, accelerates like crap, so take it to shop thinking it's time for injectors.
- Shop somehow cannot figure out which injector is causing issues (should have been first warning sign) so since it's been roughly 80k+ miles and I do not know when the injectors were replaced last have them replace all of them for just under $3k. Also thinking and fearing that a bad injector could take out the FICM and subsequently then take out more injectors with it? (heard that somewhere). So get it back, starts on a dime, no roughness after first starting, loving it, but now the turbo won't come down from 20 PSI cruising. Then take a look at my wires underhood to see if all was hooked back up...nope! They unplugged my EGR and the EBP sensor *head smack* and never plugged either back in. So plugged in my EBP sensor, turbo immediately starts cycling vanes like normal again, but then the values start spiking all over the place, making the vanes contract and overboost, but I caught it quick enough and let off the accelerator.

So have to unplug sensor and take it back to shop (2 hours from me, yeah, Wyoming..) tell them think the EBP sensor is plugged up and why the heck did they unplug my EGR?? Guy says that's normal, I say no, then my temps and fan don't operator normally, argues with me, says no, I say fine whatever, take my truck back, after they wanted to do more 'testing' to find the true cause. Took it back home, replaced EBP sensor myself, fixed.

Present:
Started to have issues with hard shifts on every shift now, only shifts nice half the time, and getting flares from 3-5 shift. I say all this because through numerous shops in Wyoming, and even Colorado, have had very bad luck and very uninformed mechanics that just don't know their sh*t or refuse to run through proper diagnostics or just LISTEN to the dang customer.

With all that being said, can anyone recommend either to rebuild or replace the 5r110 in my truck, if so, where would you recommend to go for a shop for rebuild or replace? I'm on the fence, because I just don't know if the core of this transmission will be okay or if a re-manufactured one is the way to go.

Should also mention these problems were exacerbated when I had a new fluid exchange done at a ford dealership last year (2018) and they use the 'new' Mercon fluid instead of the Mercon SP, I drove it that way for a week, realized oh snap! they used the wrong fluid, took it back and made them exchange the fluid for the correct fluid, maybe the damage was already done though...

Appreciate any suggestions
 
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