You would be amazed how much vibration can be caused during acceleration or even idle because of engine sludge, gunk and clogged ports.

My 2.8 is great when you step on the gas but during idle I can feel the idle jump between like 550-700 rpms. Its a little too jumpy and I know that this is related to CEL Code P1423 (secondary air flow too low bank 1). What happens is the head gets clogged on the EGR port and the sludge or carbon build up wont just break off. This causes the engine to idle poorly but its okay I can live with it.

 

I don't have a manual tranny in mine but maybe if one of your synchros are messed up it will cause vibration or would that just render the car inoperable?