Cracking panels sounds a bit alarming, would like to see the photos. It does sound like there is a problem elsewhere with the chassis.
My 94 chassis would creak and flex if driven over humps at an angle, the rivet holes through the ali panels had opened up allowing things to move around more
The old transmission tunnel does not really do much other than cover the propshaft. The newer one with the centre handbrake does provide some torsional stiffness to the chassis.
Nick