Comparing auto to a manual?? Autos are very slow off the mark.

IIRC I met your dad a while ago, and he also had the back seat out (25 kg), and the longbodys are about 100 kg heavier. This will affect your acceleration compared to the shortbody, auto or manual. (125 kg = 8% of the mass of the vehicle). May be nothing wrong at all...

Rattle under the seat is a heat shield around the cat and exhaust, a couple of large hose clamps around each end of the shield usually stops the rattle. (they are only tack welded on and come loose with the thermal cycling of the exhaust)