Sorry to hear about your problems. I put a kicker into my 2005 a month or so ago so I know what is involved. I also have a tool that holds the clutch basket so you can get that big nut off without busting your clutch basket (sorry that I am too late for that).
Here's an offer for you. I have a extra clutch basket that you can have and I would be happy to help you with the install. I'm not too far away from you if you could get your bike up here we could work on it here. If you can't get your bike here then maybe you could swing by and I could show you what to do and send you home with the clutch basket and holding tool.
Try raising the rear wheel off the ground and moving it back and forth while trying to move the shift lever into neutral. The increased leverage may help. I believe that that ball bearing goes on one end of the clutch actuating rod, but I would have to check the manual for sure. That may also explain if the clutch is not disengaging and not allowing you to get it into neutral.
Don't get too discouraged, we've all been there before. Let me know how you would like to proceed.