All Small Six Engine knock

This relates to all small sixes
I have a 1966 200 I6 that I acquired as a core, had the engine rebuilt by a reputable shop, and I installed the motor on my 1962 Comet with a 2-speed Mercomatic transmission. The build happened 2 years ago and I'm just now really getting serious about getting the car on the road. I've put about 50 miles on the rebuilt engine. It's got a knock. I thought it was top-end noise, A mechanic adjusted the valves, set timing, adjusted the carb and the motor became much quieter but still knocking. The mechanic thinks it's bottom end noise. I took a stethoscope and the noise was loudest over the oil pan beneath #4-6 cylinders. Dipstick oil was fine (still has break-in oil in there. Oil pressure with gauge was 50 at idle, 60 when revved. I pulled the flywheel cover and checked the flexplate (new install with rebuild) and couldn't see any cracks. I pulled the oil pan - no metal or glitter in the pan. Thinking it was a rod knock, I pulled the caps off #6 and #5. The rod bearings have light, mild scoring which I can't even feel. All the surfaces are getting oil. I checked #6 bearing clearance with Plastigauge and got .002 (spec is .0008-.0024). I haven't checked the other bearings as I'm not sure that's what I should do. I'm about ready to pull the motor and haul it someplace for a teardown. Any ideas? Thanks!
 
That makes sense. I looked closely to see if there was evidence of metal impact in that shallow area and didn’t see any but it could be just barely touching. And the pan is ever so slightly dented in where the steering center link crosses the pan. There’s only about 1” of clearance between the pan and center link. Is it possible that at some point the car hit a bump or pothole and pushed the center link up and dented the pan? I’m going to push out the dent and put things back together and see if that helps. Thanks!!
 
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