What do you mean it runs rough? Does it seem like it's misfiring or is it just vibrating? It's common for the tranny mount to go bad and allow the transmission to sit on the engine cradle. This will cause a vibration that would be worse at idle, in gear at idle and when the car is under load like with the a/c on. It tends to be confused with a misfire. You would really feel it through the steering wheel. If it's misfiring the dealer should have been able to come up with something because with the OBDII diagnostics it in most cases is sensitve enough to point you to the right cylinder(that is if it is misfireing). Low or high fuel pressure can cause a car to run rough. You can check the fuel pressure at idle and at various RPMs. At 100K you could be looking at a fuel pump or a bad pressure regulator. Also vaccumm lines should not be over looked, but in most cases a vaccumm leak should show up with a code scan.
