Bob,
I've spent hours fiddling with the estart system. I've changed the tooth profile and polished the gears. I've spaced the cover out and spaced the starter out. I've added the Ballistic 8 cell battery which has way more cranking power than the Shorai.
It sounds to me like your side cover was spaced too far out, but I'd need to see pictures to say for sure. Even though the bendix cams out when you try it with the cover removed, it still can misfire. What I've come to learn after trying Roscoe's spring stretching, is that it's a balance of forces.
Think of it like a pistol: the slide return spring must be correct for the bullet weight and powder charge. You can "tune" a pistol for better function. The same thing is true with the starter. Just because the bendix cams well doesn't means it will engage fine.
1) You have be sure the basic tooth clearance is correct by shimming the cover (crank location can vary a bit when the engine is assembled).
2) You need a good battery and quality connections.
3) The flyweights must fling out quickly to develop the inertia necessary to force tooth engagement.
I found that no matter how perfect everything else was, the flyweights are the key to good operation. The bendix cam groove doesn't have enough push to guarantee that the gears will mesh. The pinion gear can spin up in rpm before the teeth mesh and then you're screwed. This means the pinion teeth sit against the ring gear and grind until you release the button. Mine would only work 50% of the time. Polishing and profiling improved it 70%. I've only had one ride since I stretched the spring, but the system functioned 100%.
That's right, it never missed once on the approximately 20 starts during the day. So the conclusion is that the flyweight spring controls the initial advance of the gear which is critical for tooth engagement. Ideally the teeth should engage before the starter motor even gets up to speed.
If the flyweight spring was available as a spare part, then experimenting would be less risky. I rolled mine down a long neck bottle to a diameter of 2.250 inches. This seems huge, but it worked for me. It sprung back so close to the original ID, I could barely measure that it changed. The spring is very delicate, so you have to be careful.
The system can be made to work. A good dealer should be able to do this work if you are reluctant to fiddle with it. And yes it should work better as delivered, but no company gets everything right, every time.