Yes ,reach around to the other side of the bike and push the bolt back in. both of the bolts that hold the peg plates run through the motor from one side to the other ,when you remount the pegs again these two should be torqued( you'll need a wrench on both sides) as they also hold the center cases together and if not tight the case seam can leak when the bike is running. the bolt slid back because the bike is leaning on the side stand.
    When you try to loosen the nut ,doesn't the clutch basket move? this is the movement your trying to stop.    If you look down below the cam chain tensioner  ,there are two gears that nearly touch ,one being the gear on the basket .this is where you need to place the nickel ( but a piece of alum. would be better as it is softer than the gears and not tend to damage their teeth) the "shim" needs to be placed above or below  these gear teeth to jam them ,  depending on if your loosening, or tightening the nut.
   You should invest in a Clymer book ,the money is well worth it.

Is the bike in neutral?   If it is try putting it in gear ,that should force the gear on the back of the clutch basket and the gear on the motor's main shaft to turn , (be gentle you could rock the bike off the kick stand)  then decide where you need to place the shim. If that doesn't work you may have to wait for others to chime in as I must admit to never being in the clutch on my bike in the 25 Years I"ve owned it.

The reason you are not moving the primary drive gears when you turn the clutch-hub nut is because to access the nut you have to remove the release plate.  The release plate, item (14) of the illustrated parts breakdown, is shown in this picture.

Don't put a nickel in the primary drive gears to lock them.   A nickel is too hard, you're gonna damage the gears.  I suggest you go to the hardware store and purchase a short length of 1/4" soft-rolled copper tubing.  They typically sell it by the foot.  Soft-rolled copper tubing is annealed and dead soft.  It works great for locking the gears.  You need to lock the primary gears when you remove or tighten the primary drive gear nut.  That's the nut on the end of the crankshaft.  It's left hand thread.