Heat is the angle most guys miss on these. That welded nut trick works great but you can make it even easier by hitting the stud with a torch for maybe 15 seconds first, just enough to break the rust bond, then let it cool for a minute before you try backing it out. The heat cycles loosen things up way more than brute force ever will. On an F-150 frame you got to be careful though since you don't want to cook any nearby wiring or brake lines, so keep a wet rag handy to shield stuff. Your mileage may vary depending on how rusty the threads are, but in my experience a little heat plus the welded nut is about as good as it gets in a tight spot.

Six years of doing this and nobody caught it" is wild because every shop I have ever been in has at least one guy who will lecture you about the correct way before you even finish rolling the bike in. Honestly though, you are not the only one who learned it backwards, almost everybody clamps the cable first because that is how the videos do it and the videos are mostly made by people who never touched a bike with a bent hanger. Setting the limits with zero tension just makes sense once you think about it, you are stopping the cage by hand instead of letting the cable fight you the whole time. The barrel adjuster thing is the real giveaway too, if you are maxing it out just to get shifts, something upstream is off, not the indexing. At least you found out from the old guy and not from a customer bringing the bike back mad, that would have stung way more.