I did some more diagnosis last night. With both belts removed, the sound is still there, kind of figured I wouldn't get that lucky
Using a piece of rubber heater hose as a "redneck stethoscope", I ran the hose all over the engine. I put a ear plug in my other ear to block out background noise. This is what I found:
Valve cover - quiet, no unusual noises
Cylinder head - checked around/between all the spark plugs, no unusual noises
Block - from cylinder head down to oil pan, 1-4 completely quiet.
5 and 6 I can hear the noise, down low by crank
Oil Pan - quiet, except at the sump, you could hear the oil pump pick up sucking oil
I got below the engine, laying on the ground, the
loudest source of noise comes from the bell housing. With the hose touching the bottom part of the bell housing, directly below the flywheel, this is where the noise is loudest. Moving backwards, to below the clutch, silent. The transmission is silent, too.
With the engine running, I removed the dust cover form the front of the bell housing. Putting the hose right at the oil pan/RMS/crank flange/flywheel, this seems to be the source of the noise. You can hear this noise on the bottom front of the aluminum bell housing more then on the engine block. Maybe because aluminum transmits the sound more then cast. Like I mentioned above, I can hear the noise on the block at #6, and less so on #5.
When I last pulled the transmission, the flywheel was tight, no cracks visible. I do not have any strange sounds at start up/shut down, which would be typical for a loose flywheel??? Clutch engagement/disengagement does not change the noise. I did not check the flywheel with a dial indicator, but when I pushed/pulled on the flywheel, I could not feel any play. I do not think I have a loose/cracked flywheel, and the thrust bearing portion of the main bearings I would assume to be fine

With the dust cover removed, engine running, the flywheel appears to be running true/straight. Looking at the gap between the ring gear teeth/inside bottom of bell housing with the engine spinning, the gap remains consistent, no wobble or any other abnormality.
The harmonic balancer on the front of the crank looks to be fine, no noise at the front of the engine, or timing chain area.
The noise I am hearing is more of a "tick" then a "knock". I have heard a rod "knocking", right before it went through the block, the sound I have is definitely not that. People describe "piston skirt slap noise" like a double tap. My sound is a single tick, consistent with RPM. The "tick"
does get louder as RPM increases. The "tick" is audible at idle and all RPM ranges. I have noticed a vibration coming from the engine that was not there before. When driving the Scrambler, you can't feel the vibration. But, with it sitting in the yard, holding a steady 1,500 RPM, you can feel a slight vibration.
The engine runs fine and has good power. It does not use any oil. It has been a couple thousand miles since the last oil change, the oil still looks new. Besides the "tick: sound, no other issues or strange sounds.
So, not sure what is causing the "tick"/vibration, but I would assume it is down low in the engine, either main bearings or connecting rod bearings, or loose rod bolts
Probably no way of knowing without pulling the engine to pieces. I won't have time for that between the South Dakota trip coming up soon, and Sand Blast at the end of July. I might not get back to this one until the fall. Whatever is making the noise, i don't think it will be cheap.
Too bad I can't get a new 258 long block for $1,700, like I did with the GM 350 in the tan Scrambler
Any suggestions for further diagnostic testing, thoughts or opinions, will be appreciated
