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Correct me if Im wrong but I think this is the two culprits
The shoulder bolts are more or less there just to help with assembly since they hold the plate in place while you add the 4 other screws that are used to tighten the z axis plate down. It is those 4 screws that also need to be loosened and shim to be added behind that plate to adjust nod. Also note you have to have the z axis all the way up to access all 4 screws.
You are correct, it took me a LONG time to realize that the z axis must be raised to the top so the bolts can be loosened. After the two shoulder bolts are loosened along with the 4 screws, it is necessary to lower the z axis and adjust to the correct position with the tramming arm. Or so I think!