I have one complaint about the mach 460 system in my 2003 mustang. Although it sounds great ford needs to re-evaluate the insulation in the door panels. It makes the system sound ****ty when theres a lot of bass, because the door panels rattle. I think I need to buy some dynomat big time.
There is a wiring harness in the door (going to the window motor, I think) that has a plastic tube around it to prevent it from chafing. The tube is just loose, and it rattles like crazy when you have big speakers in the door. You can use electrical tape to anchor it down, or just cut it off. It's in the middle of the door, behind the inner panel of steel. You'll need to remove the inner door panel to get at it.
You shouldn't need to use Dynamat in the door with any factory system. It's needed mostly for large areas of flat steel that are near woofers driven by a lot of power.