I put my Ford dealer-rebuilt trans to the test again yesterday....full slick, 4500-5000 rpm clutch drop, 8 or 9 passes. No problemo. Then again, it was shifting fine even before Ford rebuilt it, ha! the rear still whines a touch in a narrow speed range, 120-140 Km/h but, not enough for me to get bent about it and lose my car for another month. Eventually, I'll dynamat the spare tire well as that seems to be the speaker for this noise as, when I piled a bunch of loose high density foam in there, it diminished some.
That whirring noise is the throwout bearing and isn't an issue, Gabe, unless it's really screaming or chirping. The rattling I can induce occasionally in 1st or 2nd when I don't stoke quite enough rpm on it and lug it slightly. Try a higher gear just so you're not chugging it at 1000 rpm. GT500s have along list of people bitching about the trans too; don't assume all your problems go away there.