Delta, this is a problem I've been trying to deal with for some time. I know you've read my build thread, so you know what a stickler for accuracy I am... but some of these things don't reconcile themselves very easily.
As to the brake stay (stopper arm) hardware, I was just as confused as you are. The pic on P. 72 seems to indicate that the rubber washer fits against the brake plate, while the pic on p. 76 shows it otherwise, with the stay against the brake plate. That same photo is repeated on P. 16, fig. 35. And if you look on P. 17 fig. 38, you see the set-up from a slightly different angle; it, too, shows the stay against the plate, with the rubber cushion on the outside between the stay and 18mm washer... so two different photos in the manual show it this way opposed to only one of the other...
The Owners manual shows yet another pic from a different bike, again showing the arm against the plate, then the cushion and washer. Note, too, that the nut is kept in place using an "R" pin rather than a cotter pin...
I finally found some shots of a low-mileage, unmolested CB550 and it, too indicates that the stay should be on the inside, with the cushion and washer on the outside. That's four different references showing it this way, so that's how I assembled it on my bike. I figure four-to-one odds are pretty good to suggest that's how Honda really did it.
I had the same frustrations when it came to the brake lever adjuster bolt. P. 76 fig. 235 clearly shows the bolt inserted from the top, and includes an inset to emphasize the fact. However, the Owner's Manual and just about every stock CB500 and 550 I've seen have the bolt inserted from beneath, with the head of the bolt resting against the lever.
I figure in this case, since Honda shows it both ways, it doesn't matter; so I chose to insert the bolt from the top to give myself a little more adjustment room.
The 92mm O-ring fits down around the retainer, and the side plate covers it. I believe it's meant to keep moisture from getting into the retainer threads.
Hope this helps, from a fellow detail freak!