AZ, the noise is probably normal. The manual trannies in our V6 mustangs are not refined, nor world-class, nor close to the better manuals of other makes. It makes all kinds of whirling noises, and is clunky, to be sure. Relax...this is normal. It is a bad design...I've driving many manuals from Mercedes, BMW, Toyota, and especially Honda, and VW, and those all were often more refined, and world-class. The one good thing about our V6 manual trannies is that the gear ratios are near perfect. I love my car and have no regrets, but it is what it is, and I knew this the day I bought it...Relax...I strongly suspect your car is fine. It has a louder then normal throw out bearing too, and the shift action is knotchy...all normal SADLY.
I miss the smooth silky sure footed action of the Honda and Acura manuals, and the BMW manual I once drive was a dream.