Most of the fairing "bolts" are called Truss Head Machine Screws (5mm) and can be had in zinc plating from any good hardware store. Freestyle Don Cortes probably has them in OEM black, and maybe in silver color, like the pair found under the headlight. (Don prefers official Honda part names and part numbers.)
The clip nuts are 5mm, and I've not yet seen them new. Don would again be a good possibility; they are not used on Honda cars.
Six millimeter Flange Bolts are again standard hardware, but the ST's Spring Nuts (6mm) they mate to are not. (Standard automotive U nuts are seldom used by me for an ST.)
What other clip nuts or special bolts are there, not covered above, but needed by the Thread Starter? (Again, descriptions from an ST1100 parts list are preferred.)