Thank you so much for your reply, Orange! It really made my morning.
There are various notes I can impart that I didn't think to include in my first write-up.
A word of caution: If you have a board mostly feels good, I'd recommend against doing this. I had fun and don't regret this project, but I can easily see the cost being a lot higher than one may desire or expect. (A swapped in switch can easily feel good one day, and the next day it'll be too light/heavy).
...but if you ignore the above caution, end up learning from this thread, and modifying the layout or use it outright post about it elsewhere, please link back to the thread and let me know? (Even if it's years in the future.) Something that drove me to finish the project for the last six months was the idea that others may do this more after I post what I did with my layouts. It would be cool to see some ripple effect from this.
Labeling: To label my switches, I've relied heavily on fine-tip sharpies. I put abbreviations on the bottom and on the back of the casings: spring type on the bottom and the case type on the back of the casing. I've included a picture of that to this post. If the case has a black bottom, I can label the upper plastic, but it will wipe off easily. On Box-style stems, it is possible to put abbreviations on the top of the stem (notably on the east/west sides of the stem; all labels on north side will wipe away quickly).
To answer your question about organization, There's a lot of context that I need to give else it may not make much sense.
Notes on switch components: My ability to understand how I was modifying the switches changed over time. I did most modifications on on Box-style switches due to the variety of them that I could easily modify.
For Box-style stem switches: Springs and Casings: For these switches, springs have the most significant impact on if I was bottoming out or not. Once you have a rough feel for where you want the spring weight to be, you can then modify that weight up or down slightly by changing the casing. With MX-compatible cases, I felt that weighting roughly worked as Box Brown < Hako Violet < Hako Clear < Hako True. NK Royal cases would fit between Violet and Clear, but they would also develop clicking noises as time goes on, so I stopped making those modifications. Burnt Orange cases provided too much tactility for me.
Tactile Box-style cases have a brown nub in the case, whereas clickies and tactiles have green. Tactile MX stems are the same as linear stems, but with a small notch cut into the back which hits the nub for tactility. Clicky stems have the same stems as linears, but they have additional plastic in the front to engage the click bar. If you put a tactile stem into a tactile switch green nub case (such as with a Hako Royal Clear or Kailh Silent Brown), there's somewhat of a click bar feel where you can feel a slight bump as you press it (but that bump is not necessarily at the actuation point!), presumably due to shape of the tip of the nub (as green is more rounded, but brown is more angular). I didn't want this feeling as I gamed, which is why there are not many switch types that use this scheme on Variants 2 and 3.
Stems: On a Box-style switch, the stem modifies how keypress feels. I don't have a great vocabulary for it. A Box Brown stem feels like a short press, bottoming out faster than other stems. A Hako Violet stem feels like a sharp press with a sharp bottom out. A NK Jade stem feels like a sharp press but with a slightly muted bottom out. A Hako Clear stem feels like a sharp press but with a more muted bottom out. A Royal stem feels like a deep press which goes on for longer. Burnt Orange stems are very tactile. I think that most poeple won't quickly notice a difference between differences here; I know that I prefer the feel of a Violet stem, followed by a Jade stem. It is something I think most people will only notice if they pay close attention to what each keypress felt like as they type. (I don't recommend that; it really contributed to the overthought part of this project since as I type thoughtlessly, things usually feel fine, but if I really pay attention, I may decide to make all softs of small changes.)
Overall: When working to figure out Box-style switches, I suggest figuring out what type of stems you enjoy first, and then figure out spring weights, and then swap around with modified cases. If you can't get the keys to feel right even after going up/down through different cases, then change the stem type and revisit.
For Cherry-style stem switches:
I have a lot less knowledge here about how stems and cases change the experience for a Cherry-style stem switch. The stem doesn't feel like it changes keypress feel as much as it adds an additional modifier to the spring weight that you've selected. Kailh Purple feels a bit tougher to press down on, whereas a TTC stem feels super light. A YOK Purple stem is in between that. When working through Zilent modifications, changing the stem felt a lot like changing the casing does for Box-style stem switches.
Organization: So, Orange, to answer your question about for organization: lots, and lots, and lots of plastic baggies. If you're going to put a toe into the water, start by modifying switches by keeping the same stem/case and changing the spring weight, and bag those together. (Hako Clears with different switch weights in one bag, Pro Purples with different switch weights in one bag, etc.) When you have specific stems that you enjoy using, as switch count increases, consider putting switches into smaller plastic bags (which lives in one larger plastic bag) based on stem and spring weight so that you can swap switches based on small differences that you need. (Hako Violet stems with Royal springs in one bag, Hako Violet stems with Pink springs in one bag, etc.) Modify this scheme as you find useful; a deviation I made was to put all my modified Zilents into smaller bags based off spring weight instead of stem.
