Cool project! I like the overall number of keys, the focus on getting good use out of the thumbs, etc.
I’d recommend trying to make a few physical mockups (e.g. by mounting switches in a piece of cardboard, or even just sticking keycaps to a paper with some double-sided tape) before settling on a design to wire together. I’d likewise recommend trying to get the physical shape roughly figured out before worrying about the logical layout.
My thoughts about the physical layout:
* The bottom row keys there are going to be somewhat slow for fingers to reach. Keys two rows above the “home” row will generally be easier than keys two rows below (especially if you have sculpted keycaps). In particular the pinky is going to have trouble reaching either two rows up or two rows down, but there’s space for 2-3 keys to the outside of the pinky home position that are very easy to reach. Likewise the index fingers could pretty easily reach another inside-column key if you want.
* I assume the lower vertical keys are for the thumbs? Those are going to be very hard to press over the tops of the other keys you have, unless they are substantially taller. Same story for the commodore logo keys.
* In general your thumb keys are laid out in a pattern that seems a bit unlike the way my thumbs can most easily move. All of them could be pressed, but it would require moving the hand forward and back or else stretching it out and flexing the wrist, and I’m not sure how comfortable it would be to use those as modifiers (though if you always use the opposite-hand thumb modifiers for a particular finger key it might be fine). I’d recommend mocking up 3–4 different configurations and testing to see which one(s) work best.
Some thoughts about the logical layout:
* Personally I’d generally recommend against layers that you need to toggle on or off, in favor of layers that are active while you hold a key or keys down. But you should try both ways out and see how well it works in practice. I find that I personally get very frustrated with toggle-type layers. In my opinion toggle layers are best reserved for you have some context where you spend extended periods of time only needing the keys on the toggle layer, for example you could make a “photoshop shortcuts on one hand” toggle layer, or a “spreadsheet data entry” layer, or a “video game X” layer. Especially in cases where you need the other hand for a mouse, pen, or other input device, this can be a great help. For regular typing though, I much prefer hold-the-modifier layers.
* As a corollary to the above, one of my personal methods that seems to work pretty well is to have a thumb key on my left hand as a "function" key, and then use the other keys on my left hand to pick out a particular layer, with the layers themselves being on the right hand keys. If I use chords of left-hand keys to choose the layer, this gives 16 different layers using only chords of the thumb plus 0–4 home-row keys. If for whatever reason 16 layers is too few, I can move all my left-hand fingers to another row and get another 15 layers. Then I don’t have to be shy about adding tons of layers, and it’s easier to keep everything I need nearer to the home position.
* I think the numbers are going to be a bit annoying to type in the middle of text (comparable to a standard keyboard maybe, but that’s a really low bar).
* I would not recommend having the up/down keys be on opposite fingers on the two hands, it’ll be very confusing to remember. Also, if the arrows are going to be on a layer, I’d recommend putting them near to the home position.
* I suspect having opening and closing parens/brackets on opposite hands will end up being annoying, especially if you need to stretch one of your pinkies down to hold the fn key for it.
I hope none of that sounded too negative. I think you’re on the right track, and I’m sure after you’ve tried some ideas out you’ll have a better idea of what works or doesn’t work for you personally.
Good luck!
