Sean, I watched some of your video. It appears Lionel replaced the springs that were used on the rear axles with the brass plate(s) that you found. The reason the rear axle now has more vertical movement is because I assume you left them out. All the previous Moguls had springs which pressed the bearings against the bottom plate. You want to have either springs or plates over the rear axle if you want all six wheels on the same plane against the rail.
Pete