Well, the tranny shouldn't go into all the gears freely without the use of the clutch. That sounds like your clutch is slipping really bad. That has nothing to do with your tranny being loud, however. Unfortunately, that sounds much more like a bad input shaft bearing. I would certainly believe the T45 is goin on it. They haven't been any more reliable than the T5 from the posts I've seen.
As far as the rear end groaning, what do you mean by groaning? Have you checked the fluid level in the pumpkin? Does it leak any lube out the axle seals? There really isn't anything back there to "groan" other than a dry clutch pack if you're out of fluid. I would change the fluid back there. If there is a whining comeing from it, that would be the pinion bearing.
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