What causes back pressure on a 2003 ford escape?

I have a 2003 ford escape 4x4 3.0l v6 that the shop says has back pressure. I took it to a muffler shop they put a $1,200 catalytic converter on it and said it was fixed. When I took it back to the transmission shop he says it still has back pressure and when he pulls an o2 sensor it runs better through the open hole in the exhaust letting out more air what causes this? it is making my car down shift and then it is not able to up shift cause it isn't pushing out enough airflow. The muffler shop said that the flow was good and there are no clog. What is my problem?