So as mentioned earlier in this thread, I wound up running a 1mm oversize YZ465 cylinder giving 476cc.
One thing to watch out for is the base gasket. The later version Yamaha (and some aftermarket gaskets) have a sealer as shown below. This is an improvement on earlier gaskets with no sealer.I became aware of this issue when my IT490 developed an air leak using one of the earlier gaskets.
The cylinder head was painted in silver enamel and baked in an oven.
And then the motor, with assembled top end, was bolted back into in the bike.
The stator plate was pretty dirty...
I used contact cleaner to clean the plate and various ground contacts. I also cleaned and checked the mounting screws and wiring harness. I did not go overboard on the coils as I did not want to stress the wiring or insulation.
After cleaning, the stator was mounted to the engine and the timing marks were aligned as specified in the manual.
Both crankshaft and flywheel tapers were carefully cleaned. A light grinding compound was then used to lap the tapers together to ensure a tight fit. The tapers were cleaned again and a new flywheel key was used when mounting the flywheel for the final time.
I could not find my flywheel holder tool so used the old tie down flywheel holder trick.
Using a tie down, hook one end to the frame then make a couple of wraps around the flywheel like this
Hook the other end of the strap and pull up tight.
Then use one hand to put weight on the strap to tighten and hold the flywheel from turning while you tighten the flywheel nut
with a torque wrench with the other hand.
Sorry, but with both hands occupied, I could not get a photo of this final step :-).