Looking back at your previous posts I see where you had just the spacer installed behind the sprocket carrier that left the sprocket carrier sitting just a little bit higher. This would be how it should be. I cannot figure how the rubbers would cause any misalignment, especially with the axle installed. The only way I can figure that could happen would be if one of the wheel bearings (either in the sprocket carrier of the hub) was worn badly, or damaged in some way, or the bearing was not seated squarely. From the looks of that bearing retainer I would inspect the condition of the bearings closely. All Balls has bearing kits, and the bearing retainer I believe is still available from Honda, so replacing the bearings and retainer might be a good idea, if only for peace of mind and as "cheap insurance".