John, you've definitely made the right choice in putting the set screws over the key rather than over the shaft.
That said, my own limited (one model) experience has been that this approach has an aggravating tendency to loosen, especially on the flywheel. I also had a problem with the ignition cam coming loose; it too is also secured with key + set screw. I put blue thread locker on the set screws, and that seems to have fixed the ignition cam, and definitely improved the situation for the flywheel ... but still the flywheel set screws loosen over time. Interestingly, the gear on the crank shaft, also secured with key + set screw, has never given a bit of trouble.
I have wondered if part of the problem might be that I wound up with the fit on the key in the flywheel just a little loose - it is perfect on the shaft, but just a bit big in the flywheel. Particularly with the mass of the flywheel, this allows it to "wiggle" a bit under the uneven forces at work on it, which in turn works the screws loose ... again, this is just a theory at this point. Hopefully, YMMV!
On edit - I was looking back through the thread, and realized that I had already posted most of what is above. I apologize for the repetition. I am sure it is not age at work. I am sure it is not age at work. I am sure it is not age at ... wait, did I already say that??