I keep the bushings with the pen kits in large Plano tackle boxes. The model is 3700, is about 14" x 9" x 2". I t has adjustable compartment size. I unpack all my kits when they arrive and put the single components in separate compartments. One get all the bushings (the ones I used are out their bag, new ones stay in their bag until use). The same compartment also hold liners I make for the barrel trimmer to fit the tubes and other accessories. Drill bits are stored in their boxes next to the drill press, specialty drills for certain kits are stored in clear plastic tubes.
What I like at this Plano 3700 box is that it is reasonable priced (I think a six pack of them is about $15 at Cabelas) and they can be stacked six or even eight high in a shelf, I make the sides with the appropriate pen kit/plating name.