I just wanted to come back and update, since this was not a straightforward diagnosis!
I ended up getting an Autel MX900, and that helped a lot. The truck isn't latching misfires into history, but I can watch it count misfire cycles at low speed but not record them.
I swapped all the plugs and coils and wires around, to try to induce a predictable misfire, including indexing the plugs, with no luck.
I ended up changing the oil, and noticed a fuel smell, which was a good clue. On that symptom, I disconnected the PCV system and capped the vacuum and the idle got a bit better, and the fuel trims went up. Meaning the crankcase had fuel vapors.
Long story short, the dealer I bought this truck from, took delivery 8/23, and I bought it 11/24. You can guess how long that fuel sat in the tank and lines - and most importantly injectors! I suspect the injectors are just so dirty, the fuel trims are responding to horrible spray patterns (incomplete burning) by pulling fuel, but even then I likely had some cylinder washdown getting into the oil.
So I made sure with the scan tool that the HPFP wasn't leaking by doing a shutdown test. You run the motor and look at rail pressure, then turn the engine off but keep the key on, and watch the rail pressure. If it rises the system is sealed and is expanding from fuel soaking up heat in the engine V. If the pressure falls that's a leaking injector or HPFP.
I've run a full tank of fuel through with 3 bottles of techron, and it seems to be getting better, but another thing the Autel lets me do is an injector balance test, and it's still pretty uneven. Hopefully techron is all I need and not new injectors!
Pic of the truck, just got new wheels/tires. I bought the wheels because they're 4500lb rated KMC's, and the red color was wayyy cheaper, but it's starting to grow on me.