Methinks it might be worth - if the timing pinion slips while the nut is being done up - lightly dressing the taper on the armature shaft and the cone in the pinion on the bench to make sure they are both burr-free and clean. Also, a very clean thread (worth alway running a die down it) and a very clean nut, preferably a new one. A little cleaning, fine emery paper will do, can go quite a long way, even though the thing doesn't look much different for it. Ideally, you should be able to press the pinion on the taper gently by hand to the point where it engages enough to take nut and spanner (wrench) without going for a walk. In which happy case it's perfectly OK to hold, gently, the cb centre bolt with a 4BA (or 1/4AF) box or socket spanner, while the pinion is lightly pushed on at the other side and a very clean and free-running nut run up the thread to hold it. It's hard enough getting the pistons and points in the right places by whatever means, without having to guess what error will introduce itself while you do the thing up. Although some people do reckon a light tap works, I prefer not. Even a gentle whack can make the thing bounce, losing the setting at the cb end in the process. Plus put a new tiny burr on both male and female taper. But I agree, it's a miserable job, trying to do one thing up without disturbing another, which you can't see properly while you're doing it.
Sometimes I think it would be good if mag pinions were keyed to their shafts and a dot provided on the pinion to align with the adjacent one, as per cams. Wonder if anyone has done that? The mag would then almost certainly be model- and marque-specific. But, boy, would it make it quick and easy to put together. The downside would be lack of ability to compensate for wear on the cam ring etc. Oh, and the problems that could follow on from an armature rewind! Maybe they outweigh any possible gain, so shan't be attacking anything with sharp weapons any time soon . . . . just day-dreaming really.