That doesn't sound like a trans external issue to me.

Do you mean an RPM variable whine, only when the clutch is engaged? Did you replace the pilot bearing when swapping transaxles?

If you are running a 200k+ mile trans, that's definately the issue. Old transaxles will whine, you really can't escape it. Mine whines like crazy, but it still works so I live with it. :dunno: