AFAIK, the VUSB stack is doing USB completely in software. If you would use the ATmega32U4 as the controller you would get hardware USB support, more MPU time for other stuff and it would be child's play to adapt several existing firmwares that already have lots of features such as support for layers, macros, dual-role modifier keys, NKRO and media keys over USB etc.
One of the most popular of these is Hasu's "TMK" firmware. There is a special version of it that supports backlighting, intended for the Red Scarf II PCB (which has four columns to the right instead of just two).
I would also like to direct you to take a look at the
KPT KPT-84...
The left Shift is a standard 2.25 size, then there are 14 normal-sized keys to the right of it ... but there are 16 keys at the top row. 2.25 + 14 - 16 = 0.25 difference.
The secret is not in the keycaps, but in the spacing between the keys which is about 1/3 mm more narrow between the keys at the Shift key-row than over the rest of the keyboard.
I think that is a pretty neat trick that would allow for the arrow keys on the right while still having mostly regular staggering on the left side of the keyboard. There are more options for keycaps, and you could also fit a 1.25 left shift for those who like ISO.
Look also at the GH60 and Red Scarf PCBs for how they support different layouts: ISO or ANSI, 1u or 2u Backspace, and different options for the bottom row. Most of these PCBs have the controller chip underneath the Space Bar, but that would require a larger space bar than the Japanese HHKB has.
If I were making a PCB without SMD:d components, I would use a
Teensy 2.0 board mounted on header pins underneath the numeric row. You would solder the header pins first, then the switches and the Teensy last.