With the Nismo R34 GT-R kit, you can use any combination of wheel and disk/hub assemblies you want. In the kit, two wheels (stock and Nismo LM-GT4) are identical in size--the width is 13mm, and the depth to the base of the pin inside the wheel is 10mm. The optional vented disk/hub assemblies (part E-3, 4, 6 and 7) have a thinner hub, but the backside where it's glue to the upright is thicker to avoid any changes to the track width, so the wheels will neither stick out nor sit inward regardless of which wheel you use.
The optional brake disks sit further out from the center, but that won't interfere with the stock wheels either, so pick whichever combination you like, and you are safe.