I had fits with getting my hubs to be straight with the crank.

The thing is the drill bit you initially used to make the hole proabably wandered. You can correct this by boaring. If you don't have one get a set of quick change tool holders. Using an Armstrong tool holder for this kind of work is an uphill battle. Use an allen wrench with a cutter ground on it to get the hole dead parallel with the lathe bed. Then cut your taper. Then make a relief at the small end of the cone then cut the threads for the crank by boaring. Then cut the threads for the prop shaft by tap. Support the tap in the tailstack. It wil be awfly close a that point. JB it to the crank. At that point I put the tail end of the crank in the 4-jaw and dialed it in. Tape the tie rod so it is not flopping all over the place. The bearing for the front end of the crank went in the steady. I put a center in the prop nut shaft to get the hub real close. At the point I turned the hub to be dead straight. I then cut the radial knurling by broaching withe the cross feed. Reassemble the engine.

Or accept that the engine will vibrate some!