Yeah, you need a slot on the right side of the shift lever for the parking brake. Therefore, another hole.
The front clip on medium-duty trucks is VERY different - nothing will interchange, except maybe the individual bars of the grille. The cabs (including the transmission covers) are the same. Either your motor/transmission mounts are really messed up, or your cab mounts have collapsed. My family has two medium-duty trucks, and the transmission in both sits just like a light-duty truck, with the exception of the slot for the brake handle. The transmission should comfortably sit under the cover plate if the cab is sitting properly. I'd get an assembly manual from the parts dealers and start figuring out what's broken.
