Your base kit contains some unnecessary keys, namely R3 1u #~ and R4 1u \|.
You can remove them and in their place add R4 1u Ctrl and Alt, which are required for covering some 40%, 60%, 65%, 75% and 1800/CP layouts. If you check, you'll see that pretty much every set includes these keys.
I think that stepped R3 1.75u Control and R4 2u Shift aren't worth including, as the use cases for these keys are fringe at best.
In their place, I suggest adding R3 PgUp, R4 PgDn for covering popular 65% layouts and other layouts that use a right column.
Another consideration would be adding two R4 1.5u OS keys and a second R4 1u Alt key for users of OG HHKB and Mac bottom rows. But this is not a must.
The R1 1u \| key should be gray instead of yellow.
As far as legends go, you should probably change that Menu key to Fn, as the latter is a more common, useful and versatile legend.
I'm personally not a huge fan of Code, as it doesn't make a lot of sense as an OS key legend imo, but I realize that this is down to personal preference.
The NumLk accent doesn't really work, imo. Consider dropping that.
The other kits have some issues too, but I think this is a good starting point.