2002 Ford Taurus rough idle

I have recently noticed an "occasional" rough ide and an "occasional" hesitation while at highway speeds.
The problem at high-way speed happens maybe 2 times in my 20 min. Drive.
Today while at idle the car's check engine light began flashing then became constant. So the check engine light is on constant now.
I have also heard what sound like a exhaust leak near the rear of the car. This is probably a muffler but though it might be of interest.

Any ideas of a solution and an estimated cost for a fix would help.