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Hello, does it run fine at idle and no noises? Did you happen to know what codes were stored when the check engine light was on? When does it make nose,when driving at a certain speed? Is the trans fluid full and look clean/red or smell burnt badly? Which engine is in this vehicle the zetec dual overhead cam engine or SPI 2.0 engine?
Ok what type of noise, like a groaning,belt/pulley type of noise?Or knocking?Does it run rough at idle?
Ok and the noise appears to be coming fro the engine? Or from the transmission Hard to say without you being a little more specific. The engine still shakes while driving, like its bucking/misfiring?
If its coming from the engine it depends what area of the engine is coming from. A loose spark plug can cause a noise and you would feel it thrugh the top of the ignition wire on top of the center of the valve cover where the spark plugs are. It could be a noise from the belt tensioner, removing the serpentine belt and if the noise goes away would indicate its coming from one of the belt driven pulleys/altenator,etc. If its still making noise with the be removed and coming from the front of the engine it could be an issue with one of the tensioner or idler pulleys for the timing belt. If its coming from the top of the engine/valve cover area it could be an issue with something in the valvetrain/base engine problem/mechanical engine issue