So my car is shifting really ruff around 45 to 55 mph and just seems really sluggish would a clogged cat make the car run like that keeps throwing a o2 code also and it sounds like the system is leaking too you can hear it clearly when you first start it

Yes, a clogged cat will (can) give you that error code but so could a faulty O2 sensor...I'd start there as it's the least expensive and then consider the cats themselves...

The flexible exhaust bellows could have broken. Your exhaust pipe couplers near the very center of the car could also be broken--the pinch bolts could have rusted through and allowing the coupler to leak.

As for the sluggishness of the car, clearing all codes is the first step. FYI, any car with a Check Engine light on is operating in "limp home" mode. This mode consumes more fuel and therefore decreases performance.

Sloppy shifting could be caused by fluid that is past it's useful life. I don't know how many miles you have, but Audi fluid is not "lifetime." It's more like 50,000 mile interval fluid.