For my pen kit storage I use clear plastic shoe boxes from Bed Bath and Beyond. The extra kits, the bushings and any special "stuff" for that kit is also in that box. If I have made up extra blanks with tubes etc., they go in the box until ready to turn.
I also use the same system for my call making, when I make duck call inserts, I make them in batches of a 12 or 24. I have one box with nothing but ready made duck call inserts, another box with ready made predrilled predator call blanks. Same with deer grunt calls and turkey calls.
In all I have about 50 BB&B plastic shoe boxes with pen kits, call blanks, call making parts, bottle stopper parts, homemade screwdriver kit parts and blanks. Each has a label on the front detailing what is in the box. If I want to make bottle stoppers I grab the box and I am ready to go to work, everything is in the box except the blank, the mandrel, the glue and finish supplies. The blanks are on the shelves in the shop, the finish supplies are in a carry box by the lathe and the mandrels are on a rack by the lathe.
For the custom pens, in that box I have all the special stuff, the taps, dies, extra drill bits with a laminated sheet for all drilling sizes and drill bits. If I buy special blanks for certain projects, they go in the box with the gear or kit for that special blank.