For a one-off I would probably put an USB hub in one or both halves. That way you give each side it's own uC, and they can probably run the same firmware. There is a possible limitation that if you want to combine the shift from the left keyboard with another key from the right side. I'm not sure whether that works with USB HID.
Adding a hub in the Keyboard also gives you options for plugging in the mouse, card reader or occasional USB stick, etc.
But why do you want to make a split keyboard at all? A popular misnomer in advertisements is that you would have to hold your wrists at "unnatural" angles for a "straight" keyboard, but that is hardly true. If you relax your hands under the table, then put them above the table and look at them, you will likely find that your pinkies are closed more then your index fingers, and that already compensates for most of the discrepancy.
I think those split keyboards are mostly like Dvorak and other keyboard inventions. They look promising on paper and intention, but in practice the difference is (almost always) negligible and not worth loosing compatibility with "the rest of the world", and that is probably the reason the alternative solutions never gain much traction. I do recognize that they can be useful for some specialized cases though.