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I replaced my right crankcase cover. Didn't have any problems removing it or taking off the ignition pulse generator and replacing it onto the new cover. The one thing that did happen is. . .the drive shaft and gear for my starter clutch fell out. It didn't look like a big deal so I just put it back in (there's a hole that the post slides into and the gears need to mesh, that's all.) But now, when I push the ignition, the starter relay clicks (sometimes once, sometimes continuously) and the tach and display cut out for a second and that's it. It won't start. But I pushed it down the street and bumped it and it ran great. But when I shut it off, same ****, it wouldn't start again. I'm wondering if that gear needs to be oriented a specific way for the ignition timing to be right or if I have some other completely different problem. Any feedback would be much appreciated. Thanks.
 

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Could it be that your battery has gone flat while the bike's been apart. I'd expect it to still turn over but not fire if there was a problem with the ignition pick-up.

Solenoid clicking is a typical symptom and dash flickering too when you push the button.

Plus it runs fine when you bumped it. Wouldn't make any difference if it was pick-up related.

EDIT thinking on, if battery is Ok you may have got something wrong with the starter gear causing it to jam up when you try to start it, and overloading the battery. Don't know an easy way to check this apart from removing the cover and taking a look inside again.
 

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The shaft for your starter falling out doesn't sound too good. I remember reading in the manual that the clicking is not only a symptom of a low battery but that the starter gear might be jamming.
 
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