I have two zipper make-up bags I found at Target that I stuff under the seat back in the tail light assembly area to hold various items. They are about 2.5" square x 9" long, made of cordura nylon and cost $2.99 each. They easily conform to the space and were both printed with skulls on them.
In them I keep two socket wrenchs (1/4 and 3/8), about 20 sockets, 27mm with 1/2 adapter stuck in it, knife, fold-up allen wrench, reversible screw driver, extra headlight bulb and other bulbs, cable ties, wire, extra fairing screws and several other random ones, and a few smaller bolts and nuts. Adjustable wrench, wire cutters, vice-grips, and pliers all smaller scale. Also a shop rag wraps the contents of each bag before it is stuffed away.
I'm a virtual shop on wheels.
P.S. - and a half used tube of RTV.