All fixed! Thanks to Andrew from another forum.
You will need to remove the long swingarm/engine mount bolt that goes right through the frame. Otherwise you can not remove #28 (bolt).
Lay the bike on its side (don’t forget to turn the gas off) with the nut upward and really soak the nut in release fluid. Leave the bike to soak overnight if it has been awhile, meanwhile go find a length of 1/2" diameter brass or aluminum, something soft. You'll need this to drive the shaft out.
All the YZ suspension bushes can be removed using the Motion pro tool and some 2" lengths of 1 1/2" internal diameter tubing. You use this to draw the old bearings out of the swing arm and knuckle joint. Water pipe works just fine. I did not have the tool so I used sockets (I do not recommend) but I needed it fixed ASAP.
I found that there was a lot of dirt in #21 (ARM, RELAY). I have it apart but #22(Bearing) did not seem to move. I good cleaning and greasing and it works fine.
#22(Bearing) should move freely in #21 (ARM, RELAY) If it does not, get the rebuild kit. Also #25(COLLAR) should move freely in #22(Bearing) again If it does not, get the rebuild kit.
Here is the link for the diagram
http://fiche.ronayers.com/Index.cfm...123/Model/YZ125/GroupID/247149/Group/REAR_ARM
I will post a new thread to summarize the process and make it easier for everyone.