I store fairing clips, plugs & screws in old plastic food containers, like Continental's 125g Powdered Chicken Stock (screw top lids), with labelling on a piece of masking tape on each container's side (e.g. "inner cowls", "side fairings"). I have also stocked up with a small store of spare screws, clips and plugs (just in case). I like the "cheat sheet" on the US forum thread
http://www.st-owners.com/forums/showthread.php?73238-ST1300-TupperWare-Worksheet but expect I'd kick or bump it and find them all mixed up
I rarely end up with unused screws etc at the end of the rebuild. My problem is dropping the little blighters either on the concrete shed floor (where they bounce or roll off into unknown hidy-holes) or down into the bowls of the bike somewhere. With ageing eyesight, creaky bones and less sensitive finger tips these days, finding these dropped bits is almost always challenging and frustrating. So I end up digging into my little stock of spares and leaving the missing ones for later.
Yesterday I arrived home from work on the bike, parked it in the shed, looked down and spotted a screw that had gone missing inside the bike over a week ago. It wasn't on the floor the day before, so clearly had survived a couple of commutes before finding its way out - bloody amazing!