To answer the original question, if you have the 4.0 you have the 42RE transmission which is a decendant of the TorqueFlight line of transmissions. Specifically the 42RE is a decendant of the A904 transmission. These transmissions had a very distinct whistling/whirling sound both on acceleration and deceleration which is perfectly normal for their operation. Most likely this is what you are hearing and it is just louder since you pulled the carpet.
My first car was a '76 Dodge Dart and it has the slant 6 engine and A904 transmission in it and made the exact same sound. It was kind of funny when I bought the Jeep this past January as soon as I drove it I knew what transmission was in it because of the sound.