Not quite sure what you mean on your first point, as the slipper pad is covered by the pressure plate and that itself is well over a mill away from the bearing holders. If the pressure plates are touching them then something is seriously wrong with the layshaft build... Thats your first port of call. Rebuild exactly to the manual first. And remember the bearing holders are handed, try them on the other side they are on atm, you might have them on wrong.
As for points B,C & D a friend had that on his 501x. He tried everything - re-shimming, adjusting, new pullies etc etc. Even thought the layshaft was out of true. What it was in the end was the original Tamiya 96t Gear was out of true. Changed to a new Associated 87t gear and all was solved. Perfect gear mesh and no major noise anymore. Cheap to try too
Its also a bit particular on pinions, a medium-long pinion work best. Tamiyas own are perfect so try that if the new spur dosent work.