It probably won't idle consistently with the CR ignition, as there's insufficient crank weight for decent idling or even proper crank balancing. Both my CR-ignition motors vibrated, and a buddy's does too; I had one of my cranks balanced by Crank Works and added a flywheel weight to the other, now things are much better.
Throwing the pipes into the fire won't clean out the spark arrestor much at all. The 'ring of fire' technique with an oxy/acetylene rig will, though.

The neutral stopper is accessible under the clutch cover. I doubt you'll have to split the cases again.
Ray