Man oh man.....

I don't think the kick start shaft will come out without removing the entire clutch basket. Easy job, just need the right tools and the manual. If you feel lost you can go to YouTube and look at how it's done. Computer age is your friend.
 
Yep! How lucky you/we are now. My first "trick" would be to put the lever back on the shaft and go through the motions and see if the spring is off of it's anchor or the spring is broken. the hint is going to be if the coil keeps turning on the shaft around the white cylinder shown in Palmer's pic.
 
I think it will come out, I just think it is a mudder phucker to put back in with the clutch basket installed. Makes the job a lot easier if it were off. You can do it. Just take your time, take pics if you have to. Like others have said you should have manual and youtube handy. Its not hard at all.
 
Someone was in the YZ I am working on right now, there is a washer between the case and the kick start shaft that was missing, I haven't yet but will be insuring all the other parts are there before I seal it back up. Damn hackers!
 
For the clutch assy you have those 6 bolts, then the nut that holds the clutch basket on, you'll either need an impact, a clutch holder, or maybe you can have someone put it in gear and hold the rear brake again, the latter has never worked for me on that though.
 
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