Thanks for including R3 PgUp, R4 PgDn. Please also include basic ISO support in the base kit (ISO Enter, R3 1u \|, R4 1u <>, R4 1.25u Shift).
The R1 End and PgDn keys can be moved from the base kit to the numpad kit, since they are always used only on layouts that have numpads (1800, CP, 96-key).
Optionally, you could also move R1 1u Backspace, the second R4 1u Ctrl and the second R4 1u Alt to the ortho & 40s kit. The reason being that you almost never see 1u Backspace on ≥60% nowadays (you can add a copy to the Minila kit, since that keyboard uses it); no modern ≥60% layout uses 2× 1u Ctrl; and the second 1u Alt isn't needed for ≥60% because there are no 1.5u Code keys in the base kit. Alternatively, you can keep the second 1u Alt and add a 1.5u Code, which together with the 1.5u Fn can be used to cover Mac and OG-style HHKB bottom rows.