Getting a clunk from the rods, need help

Measure the side play in each of the rods; there is a spec. If it is much above that spec, then oil can flow out of the rod journals too quickly, leaving the rod bearings with insufficient oil. It could indeed have been machined out too wide. This can be checked with feeler guages with reasonable accuracy with the rods still assembled on the crank. (Always check this during assembly.)

And as suggested, check the thrust bearing clearance/crank movement.