I would try replacing the plugs. My car has 96,000 miles and all of the sudden it started running like crap one day about 1000 miles ago. I looked at the plugs and they looked alright, but I replaced them with NGK Iridium IX (or something like that name) and the car runs muuuuuch better. one wire was bad on my car so I just opted to pay the $190 and replace all the wires. They just arrived yesterday so I have not installed them yet, but it should fix all rough running problems.

at 89,000 miles your car is due for a plug change, so I would try that first and see how it goes.