Pretty normal for anodizing that gets really hot. My TCE/Wilwood setup black anodizing is fading to a dark purple as well on both the calipers and hats. I wouldn't worry about it. If it drives you nuts you can have it re-anodized or buy new ones, but the same thing will happen eventually.
If that is the biggest concern you have with your Marauder you are doing very well!
As far as being disappointed in the stopping power, does that mean you just have 13" fronts and stock rear? I have the 14"/13" setup and the stopping power is very impressive. Hauls this 4200 lb. juggernaut down from speed no problem.
Lifespeed
2004 Silver Birch Marauder 130K miles
Wilwood Aero6 F, NMDP R brakes, Penske 7500DA shocks, Hypercoil 600lbs F and Grand Marquis R air springs, Addco tubular sway bars, Metco control & Watts, 31 sp axles, Stainless Works cat-back exhaust, Lidio tune, American Racing AR883 9.3" 50mm F 10" 59mm R 20" wheels, Pirelli P-Zero 265/35-20, 275/40-20 tires
Coming soon: Livernois 5.0L stroker, ADTR/Vortech V2 intercooled SC, Silverfox trans and Circle D converter