Hey Aries,
I have the same issue. I also have a 06 Coupe Black with Silver Stripes as well. Anyway, my car has 12K miles and it whines or howls as you put it starting at about 50mph - 70mph maintaining the speed with light throttle. Press the clutch it goes away or let off of the gas, it goes away. For me, it is definitely NOT the alignment. I had my car realigned when I installed Eibach springs.
I have yet to replace the rear diff fluid. I was thinking about changing the Diff fluid as well as the transmission fluid. If the whine or howl is still there, I am going to get really good at ignoring it as long as the car performs well.