I got a table top lathe over here and pulled my original crank to check it and it was over .020" runout, then I used the prybar method to true the crank and the flywheels were way off so bad you could see them moving back and forth in the lathe as it spun.
After this I used some channel locks and closed the flywheels back to where they were somewhat true spinning and isolated each crank half to bend each snout until the runout was under .002".
What I've found out is that the cranks are pressed together at the crank pin but they're not pressed in as tight as you'd think, most likely the interfearance fit is too loose from the factory so after the crank is trued by prying on the flywheels, you can actually separate then or they'll actually move on the pin. The fix is to simply weld the pin to the flywheels so you want to be sure you have a good bottom end bearing in there before welding the pin.
Once the pin is welded in place, there's no going back so you also want to be sure that the flywheels arelined up as perfectly as possible, and you have a good bottom bearing on the crank pin, and that the flywheels are as parallel with eachother as possible. Once these are set, you can weld the pin.
After the pin is welded onto the flywheels, you can then put the crank back on the lathe to true it up either by bending the snouts or tweaking the flywheels if the runout is minor. Then after this is done, you can cut the outer edge of the flywheels to get them true as well as the sides. You can also turn a small amount off the bearing surface areas to allow the bearings to slide over much easier, a slight resistance is good, but it shouldn't be so loose that the bearing just slides right on. You can also correct the bevel on the gear end if the gear is sticking out too far and not fully engaging with the clutch gear.
Once all this is done, then you'll be ready to balance the crank and it'll be ready to reinstall with a LOT less vibration.
The reason I say to weld the pin is because if you can correct the runout by just moving the flywheels by hand, it'll be true, but under the stress of higher torque and rpm, it'll just move again after installed. Welding the pin does make it impossible to replace the low end bearing, but when cranks are $25 or less it's justifiable if you get a few thousand miles on it before needing replacement. Welding the pin is not uncommon when building up a high performance Harley or Buell because the same thing, the pressed in crank pins are more stable than the bolt on pins, but they will move with the added torque and inevitable vibrations you get with a single cylinder or V twin. the weld can easily be done with a TIG welder without overheating the beraring and you should be able to weld all the way around the pin in one pass before the whole thing gets too hot.
I've also made up an aluminum block that's milled the same size to fill in the gap in the flywheels for reassembly, this combined with getting the bearing journals to where they'll slide over with a lot less force will keep the crank from bending during reassembly.
I would also pay more for a true crank if anyone was selling them, I've done one of mine and there is a lot of work involved to get them true, and to make sure they stay that way during assembly and after the engine's been run hard.
For the Hebo cylinders, the cylinder reed configuration is definitely the easiest way to do the swap, a little case stuffing might be needed tho, but going case inducted isn't that hard to do by putting the reed block right behind the cylinder between the case bolts at the base. There's also a LOT of room underneith the engine to add a reed block if it doesn't interfear with mounting the engine, and it's possible to even mount a reed block on the side of the case on the gear side, but the flywheel may block off the intake flow too much if you went side mounted.