I have been turning a lot of pens lately. Your approach would not work well for me because there is too much overlap between pen kits, drills, bushings, etc. The same drill applies to many kits, the same bushings overlap between pen kits, some pen kits have different diameter tubes, etc.
I keep the drills together in a tall "cup" along with the pen mandrels and the deburring tool. I keep the bushings together in a small "file box" in their original envelopes. I take them out as I place the pen blank(s) on the pen mandrel. I put them back in their envelopes as soon as I start the sanding step; it is important to avoid mixing up bushings. I keep identical pen kits together in small ziploc bags. "Related" small bags (the same drill size, bushings, and "style") are grouped in medium ziploc bags. I keep all the pen kits together in a large ziploc bag.
When I start a pen, I re-purpose a fold-top baggie and put the pen blank and pen kit together, along with a paper slip. I may "kit up" a number of pens at the same time, each with its own baggie with wood, pen kit, and paper slip.
As the pen progresses through drilling, gluing, turning, finishing, and assembly, I update the paper slip. When the pen is finished, the baggie has a pen and a completed slip. I transfer the information from the slip into a spreadsheet (whether good or failed) along with additional information - the recipient, date given, additional notes, etc.
The pen goes into a pen display tube along with a gift label, facing out. I find that the inexpensive display tubes make a low cost "elegant" gift container. Spouse sometimes ties a thin ribbon bow around the tube for decoration, or to attach a certificate (Bethlehem Olive, Bog Oak, etc.) .
Attached please find a copy of the paper slips, spreadsheet, and gift labels that I use. Feel free to use them, modify them, give them to others, anything you want.
P.S. I forgot to mention pen blanks. Pen blanks are labeled immediately, so I don't forget the wood species. The pen blanks fill a small square school locker of their own. They are organized enough that I can find what I want.