Hello and thank you for using Just Answer, I'm AL.
This is a common problem and it is caused by a broken band clutch inside the transmission. The only fix is to rebuild the transmission. Without this band, there will be no third gear. This will set the check engine light every time it tries to shift through third. I'm afraid there are no quick fixes. Click HERE for the bulletin Ford has issued on the problem.
Best of luck, and thanks for using JA