Rebuilt 340 knocking sound

Due process trouble shooting
I would
look closer at the oil.
Double check your electrical.
Any other mods , external clearances?

New bearings wear in , would that not explain some discolored oil as well the builder(s) may have used paints/ antiseise compounds etc.. . Were the oil pans spotless when he drained the oil . What is at the bottom of the pans or inside the oil filter?
Not enough info in my opinion for a heart operation .