I had the same ENGSYS and DEF/DPF tattletales going off - started in Arizona, and that's when I took it in to the service guys out there in Tucson. They reflashed, said it had contaminated DEF so that was replaced, and did all the past due little recall issues. I got back on the road, and all was well for a while, but a few months later it started to get intermittant amber ENGSYS and DEF/DPF faults, sometimes for only a few minutes, sometimes for awhile. I did note that at least three times, the faults seemed to be related to DEF tank levels, so I tried to keep it full and just monitor, planning to take it in later. One day, rolling down the freeway, amber ENGSYS and DEF/DPF lit up, then within a minute or two went to red and buzzer going off. Luckily I was only a mile or so from the local service guys, and they eventually found a bad NOX sensor. DEF tank sending unit was fine, and it was the NOX causing all the issues. Since that's been replaced, truck has had zero issues.
As to the transmission, I'm betting that you haven't gotten the latest software and reflash into the system. What your truck is doing is exactly what my truck was doing too, and once it was brought up to the corrected reflash it was night and day. Once that's done, it works.
The Bluetec system removal has been talked about, and the only thing that seems to have happened recently is a company in Australia that says they've managed to reprogram the PCU/SAM unit to allow removal of the system...but you have to send the chip to them to do it, which deadlines the truck. Plus of course, if the chip is damaged or lost enroute....they're pricy. So, being where I am (California), and having to deal with smog inspections every couple of years (soon going to every year, I'll bet), I just leave it installed. If it works, well, what the heck, so it's costing a few bucks and a few horsepower.
I could swear I've seen somewhere on this site a post about an earlier FG that had an Allison mated to the stock diesel, but that's an earlier system, nowhere near as electronic as ours. If I was to do it, I'd find an FG with a trashed trans, and go that route. But....lots of hours, or lots of dollars, and then time spent tweaking it to perfection. When I was younger I used to do that sort of thing, but now....time's a'wasting, and I can see what's approaching. I'd rather pay, get something that works decently (ok, so not 100%? I can deal with it), and get out in the world and see some sights, while I still have vision.
IAC, the 2012 that I have seems to be working fine now, had some decent miles put on it, went into some rougher areas, and it seems to work fine now. Time will tell though! But for now I'm happy with it.