to me the bearing damage looks to be from foreign debris. the "damage" is not enough to be causing your clunking.
you could discount this by fitting new bearings, cheap and your over halfway there work wise.
JMO. as we know, diagnosis can be the harder part of mechanicing..
ha ha! she is just...
i would check the crank journals for ovality. your bearing sizing was bang in the middle of spec, pretty much perfect imo.
ive never heard of a problem with anyone using standard sized bearings. there are multiple score marks on the bearings, including what looks like two particles have picked...