You do the LIM gaskets when you did the SC swap? Sprayed it to check for vac leaks? I'd do the compression check cause its free and is good peace of mind. Maybe pull valve covers and see if there's any obvious valvetrain issues.
I hate to say it but kinda sounds like why I'm pulling the engine outta my GTO right now. Had misfire on cyl 6 would reset and get random then cyl 5 then 6.... I did all the common stuff to diagnose it like you have plus swapped a few parts that I had extras of just to rule out faulty sensors. I'd checked it several times with a stethoscope already but decided to do it again and found one tiny sweet spot leaning across from driver side with it on pass side head I could hear the tick. After taking the head off and pulling the lifters on 6 one had chunks missing outta the roller tip and looks like matching chunks out of cam. Ran perfect, never missed a beat and wasn't nearly enough metal from the couple tiny spots to worry about bearings. But I'm pulling it to swap a 5.3 iron block just cause it's cheaper than repairing my LS1 and I wanted iron block for turbos down the road.
Not trying to scare you, but get your stethoscope out and poke and prod that thing everywhere...
