Just a thought. I have a 1928 South Bend Junior lathe with Bronze spindle bearings. I was having a chatter issue. It took me a while to figure it out. I know your lathe has Timken bearings, a completely different set up from my South Bend Junior. However, on my South Bend the bronze bearing were in fine shape. The problem was in the way the bearing were seated in the headstock cradle. I had movement when I would move the spindle back and forth in Y axis which I think is front the operator side of the lathe to the back side of the lathe. I put some brass shim stock (.001" thick) between the cradle and the bronze bearings. No more movement and no more chatter. I cannot explain why the fit was improper. Lathe runs great now.
Again, I know I am comparing apples to oranges here and maybe grasping at straws here; but while you have the bearings out, have you considered checking the fit of the races to the headstock?