"I fitted the 0.060 thrust washers on the timing side, and a 0.023 on the output side..."
I guess this is part of the mis-matched engine thing. It would be nice if there were no shims between the face of the crank and the bearing inner. Usually this is accomplished by shimming the bearing outer in the crankcase. As it stands, your shims are pretty large and heavy, and there could be quite a "hula hoop" effect as they spin around the main shafts (or the shafts spin inside them), which could cause damage to the shafts and/or the shims. In reality, if you're not going racing, it will probably be ok. But it would worry me. Maybe check with your JAP man?
You mention there is not much end thrust when the engine is vertical: true provided the piston is square and centred. You might be amazed to see the inside of an engine that has been running with a bent con rod!
Leon