Just curious...How did they "prove to you that the Amp/Amp Kit wasn't at fault?
From experience, I would be weary about taking this kind of problem to a ford dealer. And if you do, leave out the part about the recent stereo install.
Does it happen with the radio off, or on low?
Try pulling the main fuse for the amp(should be in the engine compartment 18 inches from the battery) and running the car to see if it still happens.
What kind of amp is it(brand/Model/output?), and what Gauge wire did they use in the install?