Many thanks for the comments.
I used to have coloured plastic boxes arranged on my bench for the bits as they came off but nowadays I don't bother. I know exactly what goes where and I just put them into a magnetic tray. I still use paper towels and plastic bags for brake pads, and these get labelled left and right so that they go back on the same disc rotor. Whatever works. The article is of little consequence to those of us that are familiar with it and have our own techniques. It's really aimed at people doing it for the first couple of times.
Of course, putting them into a plastic bag assumes that whoever put the fairing on before put everything back as it was ! I've had 2 ST1300 from brand new, and neither of them were properly put together when I got round to removing the fairing. So errors during manufacture or during its pre-delivery or first service must have been the cause.
Oh, yes. Although it is less easy to get it wrong on the 1300 than it was on the 1100. Honda have used different thread sizes for the different types of bolt on each component. (eg the side panel bolts. One near the pannier is longer and has a larger shoulder, so they made it a 6mm thread. Similar on the lower cowl where shoulderless bolts on the 1100 could be used where a shoulder was required to protect the plastic.
If you use the part numbers on ebay, there are a few people who get these manufactured at a much cheaper rate. I bought 50 of the shorter headed push rivets 90657-SBO-003 for ?9.00 UK. I looked again as I was re-organising the article, and they now do the push rivets with the larger head. I can't find any cheaper versions of the pin type fairing clips though.
Occasionally I just put in an order for a few of each. I hate it when I am finishing off a job and I spot that a bolt needs replacing or a clip breaks and I have to spend ages working on an alternative solution. If I have the parts in, I just throw anything that looks dodgy and replace it. Those round head, hex socket bolts with the shoulder are very soft metal and seem to tighten themselves. As soon as the socket looks a bit worse for wear, I get rid and fit a new one.