JeromeSolberg wrote:
Have you checked the bearing shells? Could one or more sets of undersize (or more undersize than you wanted) bearing shells been installed, e.g. a vendor mistake? .

You said you checked the clearances. If the crank is bent you say it only happens to the last 2 mains near the transmission. If you crank down on only the last bearing cap and the first bearing cap, the binding from a bent crank, if any, should be less. Similarly if you only crank down on the first and the second-to-last. Might be a way to understand what is happening. I still don't understand about the clunk