Base (Updated V3)
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There's a duplicate R3 1.75u
⇩ Caps Lock key in the base kit. I'm assuming one of them is supposed to be Control.
I suggest using R3 \|, R4 <> instead of R3 #~, R4 \| (incomplete ISO-UK) for the ISO keys.
Super is cool, but have you considered our lord and savior, System?
Rest of the kit looks good.
Spacebar
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The 6.25u and 7u white spacebars are duplicates of the ones in the base kit. How about replacing them with a 6u centered stem spacebar?
I don't think two 2u spacebars are necessary. One should be enough.
Consider dropping the two 1.75u spacebars. They're only used on two or three 40% customs, which, iirc, are quite rare to boot.