I think that it may be the curling that happened on the middle parts. It wasn’t a lot but definitely more than I would like to see. Most of my prints come out 100% flat, but of course there are a lot of variables that can impact the warping, and the days that I was printing those middle pieces we had a real cold snap (down to freezing) here. That made the workshop temps a little cooler than normal, and the heat would be cycling more so I think that contributed to the problem.
So I expect that it is the slight warping that is primary cause of the bearing gap.
In any case for the short term I have a workaround that will let me work with the MPCNC and once I have my printer enclosure built then I’ll work on reprinting the middle pieces that are problematic.