marker...I am trying to get the 3-rail wheels out of the truck...and...replace them with scale wheels from a set of Atlas O 100-ton trucks...so, I am pretty sure the replacement wheel sets will have the shouldered axles...what is the significance of this?
SD60M - I just converted nearly 50 cars to 2 rail, most Atlas. Many of them were wheel set changes, the rest truck exchanges. I didn't have the problem you are experiencing. In trying to understand your problem and trying to understand something I might encounter in the future, and not having your trucks in hand, the only big difference seemed to be the roller bearing rotating caps. My assumption was the the problem had to do something with that.
I was able to replace most of them by twisting the trucks to remove the wheel sets. Some had to be disassembled. I didn't have your problem and couldn't figure out why you were, but the trucks I worked with were three types of Atlas steam era trucks. Your trucks were from a later era and a different because of the roller bearings.
Like you, the reason I chose to replace wheel sets instead of using the new Atlas thin-frame trucks was because like the trucks were unique to the car. The issue with mine was color, along with black there were four or five colors. I even had a pair of green trucks on an express MKT boxcar. I never paid attention to the MKT trucks until I needed to 2 rail the car.