Annoying & mystery vibration & noise

My S350 has done 59,000 mile. From cold it drives like new, however recently after about 40 miles of driving the car starts to vibrate and a noise best described as a pump working very hard can be heard and then around town the engine appears to be running rough. I have had the wheel bearings, engine pulleys, turbo, exhaust, brakes, tyres, wheels examined but we cannot determine the cause. I always look after my car and is serviced on time. Has anyone else come across this problem and if so what is the solution to this mystery. Thanks