2001 Mustang running rough

I have a 2001 Ford Mustang, six cylinder with 99,000 miles on it. The other day the car ran fine. Today when I step on the accelerator the car lurches and run rough. Usually it happens while speeding up or going from a stop. If I keep the car at a constant speed it doesn't lurch to much but I can still feel it a bit. The check engine light came on for a bit then went off. Thought it could have been the transmission. But check the fluid and it's fine as well as the engine oil and all the gages were at their norms.
I'm now thinking it could be a fuel system problem some where. I'm just hoping it's not going to cost a lot to fix the problem. Also one other issue the passenger window won't go down if the passenger tries to put it down. And yes I have the child safety feature in the off mode.

Thanks for any help!