When I reviewed the videos I had in my phone, I realized there were two different knocking noises. The most severe was this:
https://www.youtube.com/shorts/lScIqDFrkNI
that's the noise that made me turn around and go home.
Originally, I thought this second knocking noise was the same noise:
https://www.youtube.com/shorts/R3RBycGQLAY
But listen back to back and they are clearly different.
We finally tracked that second noise down to the AC compressor. I never knew the AC compressor was even turning on. The fact that it was on intermittently explains why this noise came and went (usually with engine temperature, but maybe not always?)
The first noise may be rods, or it may be a more severe stage of the AC compressor's failure. This is unclear and may always be. We know for sure that the oil pump's pressure relief piston had some marks and didn't move smoothly. And we know the rods show some marks from making contact. But all four rods look identical and that first noise sounds like a lower frequency than four rods would make. Sounds like one rod at the most. Maybe it was one very unhappy piston in the compressor.
Anyway, to address your question, I hand-sanded any part of the journals that looked like it needed work using something very fine. More than 1000 grit, but I don't remember exactly what.
Currently, cold idle is 70 psi, hot idle is 20 psi. Plenty of pressure to keep the bearings happy.
Meanwhile, we found this problem while troubleshooting the AC system. A bad compressor is part of the problem, but probably not all of it. We suspect the control unit may be flaky, wanted to pull this panel out to look for anything disintegrating on the circuit board:

Any advice on how this comes out? I don't want to pull to hard...