I am WELL acquainted with those boots! I chased a rattling front-end noise for YEARS, tightening everything I could get a wrench on, replacing everything rubber I could find. Finally, someone here mentioned to me to check those insulators, and lo and behold all of them were missing!! What a pain! Since this was my first Mustang, I didn't know that they were supposed to be there! So yes, those have been replaced!
Is it possible that the pins are sticking slightly, causing the flex in the caliper? I lubed them when I replaced the brakes, but maybe not good enough. I also had to take a razor blade and puncture the end of the boot, because the suction was causing me problems removing the pins.