Jens77,
I'm not sure what the Honda thrust surfaces min/max were newly machined. I've lightly paged through the service manual, but nothing has jumped out at me.
What clearance does your green and blue feeler gauges indicate your thrust clearances are..?
You'll have to get a picture posted of the actual thrusts surface for forum members to actual see what your concerns are. You indicate the crankshaft has worked on them. Try a picture, perpendicular to the crankbore, of the thrust surface that concerns you.
If you feel the crank was loading on one thrust surface check for the cause. I'd inspect first the primary chain tensioner to see if it was trying to track the chain to one side. Camshaft guide for the same and replace both guides and tensioner on both. They're old. Inspect crank thrust surfaces, crank sprockets, and runout.
If you have both cranks to chose from, as pictured, the journal with the green gauge, looks very dirty with what looks like rust on the crank's bearing surface. Without visually inspecting, measuring runout, journal sizes, and magnifying it, it would be a lottery to pick the best one.
It would be interesting to know what oil was used in your two engines. One oil was up to the task. The other looks like it was not.
