So I'm working on the lower end yesterday, getting ready to split the crankcase (because of this).  I remove most of the clutch and then get to this point where I need a special tool to continue.  Fine, I say, so I move on to the other side, remove the left crankcase cover, and what's the first thing I see?  A BROKEN ROTOR MAGNET.  I go from  to  to  to  and finally to      .

Now, how did I miss this, you wonder, back when I first checked it after people suggested to check my alternator?  So I went back and looked at the old pictures, and alas now that I know which one the broken magnet is I can actually see a hairline fracture on it that I missed because it was pretty subtle and no part of the magnet was displaced.  Of course, it never occurred to me to actually physically grab each magnet and try shaking it a little bit.

Talk about tearing down your engine stupidly. 

Here's the old picture -- can you find the cracked magnet?






Yep, it's this one on the left.  You can see the crack on the inner surface of the magnet, going across it toward the back:

Sounds as though you learned a lot with the tear down...no waste there!!!   

Good thing you found it now instead of later. Goats syndrome can get messy. I have not heard of anyone having Goats in a long while.

wow that sucks but at least you found it.  I have never heard of Goats syndrome before but now that i have if mine ever starts eating itself or making noises like yours did then i will know what to look for first.  Now get it fixed and go ride

"Goats syndrome" was named by Srinath (IIRC) when a member Goat had a rotor magnet fail while the motor was running. Made a heck of a mess. This was 1-2 years ago.

  Yeah, it really was not for nothing, we all continue to live and learn, now put that bike back together and ride it, so eventually you can fix something else that goes wrong, much - much - much later than sooner though I hope. 

Goats .... yea gggggggg oooooooooooo aaaaaaaaaaaa tttttttttttttttt sssssssssssssss ... for a while there it was contageous ... ask starwalt ... he got a specifically virulent version of it too.
Cool.
Srinath.