did you check the crank without the prop hub ? The crank may need some tweeking , if you turn the hub on a stub shat ( crank) and your machine is acurate the bub should have lessthan .002 runout at the end of the hub. You must start with a straight crank and well aligned lathe. If you are going to use the fly wheel mount it on the stub shaft true the flange and mount the hub then machine it and drill the end for the prop bolt. Do all the work in one setup without taking it out of the lathe and it will be straight. Also make sure your lathe doen't have any runout.

Also you may want to use a test indicator instead of a dial.