My 1986 09 does the same thing. I've had the unit for about three years and it's done it since day one. I've done searches on here but haven't found anybody with the same problem. In a sick way I'm happy to see somebody else has this issue. I've checked the flywheel, (teeth all there, bolts tight) made sure the batteries are fully charged, have replaced the starter, done the doghead conversion, nothing has helped. It does it, no rhyme or reason to it. Sometimes you hit the key and it will click, hit it again and it will start. If on the second attempt if it doesn't engage it's time to break out the bar. Roll the motor just a 1/8 of a turn you can hear, what I think is the starter, retracting. Get back in, hit the key and it will engage. The only thing I haven't tried is to replace the starter wire, just because it is the last thing I can think of. Also, when I took the old starter in it was to a buddy who a shop for years. He looked it over and said it looked like it had a low voltage problem in the past and was not repairable. So I just bought a new starter from him and thought my problem was over. Thought anyways.
I've studied the schematics and haven't seen this but is there a crank positioning sensor in some of the units? If somebody can offer a fix I would be most appreciative.