Car runs rough at 40-50 MPH

This is a tough one. The same principles pretty much apply to all vehicles. All I can do is give you some ideas of what could possibly causing this... You could definitely have a transmission issue. Based on your description, I'd even go as far as to say a torque converter issue. Then again, it might be something such as a vacuum leak. I'm curious as to whether or not the issue could be described as a surging type issue. This would make me lean toward a vacuum leak even further. As I said, this is difficult because it could be something small, or it could be something enormous. More details are definitely need to assist in diagnosis.