Trans is unrestricted in STU.
i.e. dog boxes are OK, sequentials are OK with a weight penalty
final drive is unrestricted, differential type is unrestricted (open, clutch type LSD, helical, whatever)
Based on that, I would say that swapping the tranny that came with whatever engine you're putting in would fall under the "unrestricted" limitation.
You might have to do some customization of the CV/axles to make it all work, but that is allowed as well, as long as you keep the parts "like stock". i.e. if you have to swap one end of an axle out or shorten a factory axle by 1", that's fine. But you can't install a carbon fiber axle shaft or use ceramic bearings in the CV (unless it came that way from the factory).
Houston Region
STU Nissan 240SX
EProd RX7
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