To begin your diagnosis, you're going to have to determine the type of problem you're having. One of the most common problems is a misfire. A misfire can cause an engine to run rough or shake while it runs. Your engine has a given number of cylinders. If one or more of those cylinders isn't putting up full power, it creates a misfire at that particular cylinder(s). This puts the engine out of balance and causes it to run rough. Misfires can be caused by anything from fuel delivery to a mechanical problem. For me, the first step in diagnosing the source of a misfire is to determine if the misfire is specific to one cylinder or several. An easy way to do this is with a power balance test.