There are 3 screws that hold the factory amp. Could this "large square" you're describing be the amp? It's around 8" by 10" and has metal fins on one side.
1999 Ford Contour SVT #900/2760 (SOLD)
2005 Mazda 6s
2003.5 Mazdaspeed Protege
1998 Ford Ranger 4x4
