• I would suggest 
adding a white 1.25u spacekey to the Spacebars kit for Alice users and standard split 6.25u spacebar setups (2.75–1.25–2.25 and 2.25–1.25–2.75).
• On the other hand, I'm not sure that second 2u and second 1u white spaces are worthwhile inclusions in the Spacebars kit, as they are only used on 40% ortho boards. Either 
removing the second pair of 2u and 1u keys, or 
replacing them with a 3u spacebar (which is used on some 40% and ≥60% boards) might be a better option.
• I'd also suggest 
adding a R1 1u Backspace key to the 40% kit. This key is needed for ortho boards with a number row, such as Preonic.
• Also in 40%, you can 
change R3 1u Ctrl to something more generic, such as Hack or Meta. Explanations 
here and 
here.
• Actually, changing R3 1u Ctrl to Code would be the best option, but you're already using Code as the OS key legend. If you'd be willing to change OS keys to use System or Super instead, that'd be even better. I explain why 
here (§3).
• Lastly and least importantly, I think you can 
drop the numpad 00 key from base as that key is only useful for standalone numpads, which aren't that common, and this set doesn't have full top row support for them anyway.