my 3 door has a slight notch in tunnel to clear the transfer casing its cut into the gutter part were the bolts for the mounting go, it also has a home made box cradle to shift the box over a little for extra clearance
i dont have the half moon arch in the front chassis legs on mine, i run coilovers and its quite low and it never hits on the chassis rail so the cutouts are unnecesary imo
i also use 2wd rear diff and beam with no problems