Here is the Voice of Experience talking. I went through the "replace the boot" exercise THREE times before I finally got it right!
The inner clamp bolt MUST be on the TOP of the knuckle, otherwise the knuckle will knock the clamp off when you turn. Unfortunately the illustration in the TM shows the inner clamp towards the front of the knuckle, but the fine print states to install the clamp at the top. Tighten as much as you are comfortable, and DO use a self locking nut! I used a Nylock nut.
My clamp came with a metric nut and bolt, so I had to replace them with US (SAE) hardware in order to use a locking nut. The metric diameters and lengths fall halfway between the SAE sizes, always pick the next larger SAE diameter and next longer SAE length. There is plenty of room in there so a larger bolt is not a problem. DO NOT use a shorter bolt than what came with your clamp, you will have a devil of a time compressing the clamp enough to get the nut started with a shorter bolt!
Two final tips:
1. The TM says to bend the end of the bolt up (presumably to keep the nut from loosening). DO NOT DO IT! Use a locking nut so you can disassemble the clamp later if you need to, say to service the knuckle.
2. The TM also says to cut the end of the zipper off after you have the outer clamp in place. DO NOT DO THIS EITHER! Same reasoning, the excess zipper is not in the way of any moving parts and does no harm being there. But if you ever need to take the boot off, again say to service the knuckle, it will unzip from the cut end and you will not be able to put it together again, but instead will have to buy another new boot!