I remember this when you fitted the manual box. The end float was well over specs then. I wondered then, how long it would take for it to fail. The end float spec is 0.002", so it had gone through the white metal on the thrust, and was into the steel backing then. Sadly I agree with you that the end float has got to the point that some component, is now hitting.
I don't think it is worth doing anything with that engine. The cost of bearings alone would buy you another engine. Surly you won't be that unlucky again.
Harvey.