Peter,
If I am understanding what you are doing here you now have 3 bearings with less play replacing the looser original 2. Each of the new bearings has less freedom for the shaft to rock up and down or back and forth, or any direction. Therefore each bearing needs to be more perfectly centered on axis to allow free shaft rotation. The present bearing seats may not have that level of alignment precision, one could be off center from the rest, or perhaps tilted at an angle. Therefore when you are locking down the clutches, you are further pulling in any axially play. Now you could have a situation where the shaft is being pressed in from the sides by the needles being at different distances from shaft axis center and you are creating pinch points. I agree with Alan that you should be testing shaft rotation by hand with no worm engaged to see if you can still rotate with normal forces, and not binding up under pressure. You might be reducing shaft play, but don't have enough tolerance left for normal shaft rotation.
Just thinking out loud. You would need to test torque values to confirm what your adjustments/modifications are actually doing.
Best regards.
