Well, for me, the best way is to first mark each set with a number, there are a couple of edges/faces where that can be done without interfere with is usability. Marking then is to use something that will stay and not wear off, being easy to read, also and that is by using a engraving tool or a very small punch number set (I prefer the engraving tool), not forgetting to make a list showing what the numbers represent, have it printed and next to the bushings...!
Putting the sets in a compartment box with tags on the box, ain't going to help you if the box is tipped over, that a sort of mess that I wouldn't want to experience, particularly with as many sets as yourself so, if I had that many sets I would be building a "book page" rack, that I suggested many other pen turners with lots of bushings, to built.
What is this "Book page" rack...??? OK so, you think of how a book would look attached to a wall by its back (pages glued face), you open the front cover of a book, and go through the pages, this rack can be built with one or more pages, one page normally is sufficient for hanging the bushings while other pages can hang all your pen kits.
Perforated paneling would be needed cut at about 1 meter tall by about 6 feet wide (any size you want, really that can self support), a timber border would make it stronger and attached with a couple of hinges, to a piece of 4" x 2" previously screwed into the wall. Mounting it should be at heights that will allow you to reach the top easily.
For attaching stuff to it, hardware stores normally have available the wire hooks used on that type of panels so, you put each set of bushings in a small heavy duty zip bag, write the bushings numbers on the bag with a permanent marker and in large font, punch a little hole on the plastic bag top centre and hang it in alphabetical order so you can see what is missing.
You can use both sides of this hang panel, to hang the bushings and kits, if you have lots of kits, you can attached 2 of these panels on each 4"x2" and you can build as many of these sets as you want, if you have enough wall space. Because they are hinged, the panels swing from side to side so, then won't take any shop space when folded back into the wall, got it...???:wink::biggrin:
Cheers
George