Yes, I've been in the brake business since 2002 and ran brake clinics for various car clubs long before that. Looking at the original photos, as best I can tell, all the caliper through-bolts and bridge bolts on the front ST-60 calipers had surface rust. The rear ST-40 calipers look to be in better shape. That's consistent with spending more time and using more chemicals on the front wheels than the rear, which makes sense as there's almost always more brake dust in front.
I can't address the customer service issues you had. I like to think, if we had been in the middle, you never would have had to contact StopTech and we would have taken care of you, one way or another. But I don't know all sides to what transpired. I'll stay out of that one!
My goal here is two-fold. First, I want to see your kit fixed and looking great again, so you can enjoy your car. That's why I suggested contacting Mike Golding at ThePowdercoaters.com. He does amazing work and you may end up with better looking brakes than new. Second, I want to help others maintain a good finish on their calipers, hats, wheels, and suspension. That's why I posted a link to the wheel cleaning advice from Meguiar's. They know their stuff.
Hopefully, you'll end up with an even nicer looking car and a few less folks will have to go through anything like this in the future. Good luck and keep us posted!