1998 3800 A4 around 53k

First off....Hello every one. This forum rocks.

This started happening about three days ago out of nowwhere.
My Engine seems to be running fine. It sounds grand. The Engine revs smoothly doesn't miss. The vehicle shifts into all gears apropriatly. Service lights haven't come on. The problem seems to come when using the accelerater in Drive.
If I give it gas lightly the car drives fine until it has to shift. If I depress the pedel a quarter way down the car just feels like it's going to break.
It starts jerking and pounding; and while the car does accelerate, it's also surging at the same time. It feels like it wants to take off, but in little split second spits. I know the hesitation might be related to a clogged filter, injectors, bad plugs. But the thudding doesn't make sense
I first noticed it doing 50 flat on the express way. The car started thudding. Then it was happening when I give it gas at any speed. I know that 50mph is a shift point. I dont know if it's the tranny or rear end

Questions
Does this sound familiar to anyone?
How do you know when your rear end is going bad? What are some of the signs?
How much does a tranny rebuild usually cost?