Ok, what is the best way to prevent Injectors from clogging here then? I use only Costco 93 Octane top tier fuel. I have every fill up receipt since day 1.
Just your basic maintenance... the occasional fuel injector cleaner (I've always liked Chevron Techron). On the off chance that an injector does clog, and on the off-off-chance that it doesn't free up with a good cleaning, a new injector is $65, and takes all of 15 minutes to install - no big deal. And like I said before, a clogged injector doesn't do any engine damage - that cylinder just doesn't get any fuel, and you get a misfire. It's only when an injector sticks open and leaks fuel into the cylinder while you're parked overnight, filling the combustion chamber with enough liquid fuel to hydro lock the engine, that engine damage occurs.
In the OP's case, I have no doubt the dealership is the one who damaged the engine when they tried getting it to start. Even at wide-open, 100% duty cycle, an injector can't flow enough fuel to hydro lock a cylinder when the engine's running... it just sprays raw fuel throughout the various cycles, dumping that fuel through the exhaust, and creating quite a smoke show, as the OP found. It's not good for the cats, but that's a different issue. When the OP shut the truck down, the pressure in the fuel rail bled down through the stuck injector, dumping the contents of the fuel rail into the cylinder.
All the tech had to do, before starting it, was pull the codes. He'd see the misfire code(s), and say to himself, "self - these misfires, combined with the owner's statement of rough idle and smoke, could point to a stuck fuel injector. Let me pull the plug on the misfiring cylinder, and have a quick peek." But that requires a level of thought and experience sorely lacking in most parts changers these days.
I know - coulda shoulda woulda, hindsight 20/20 and all that... but I just have this image in my mind of a couple of parts monkeys flogging and abusing the truck without much of a clue as to what they were doing, until the damage was well and truly done - then just staring at each other and grunting cluelessly, like when the cave men discovered the discarded Coke bottle in "The Gods Must Be Crazy".