2004 has On Board Diagnostics level two (OBD2) with pretty good in built diagnostics that require a scan tool to retrieve information stored in the computer of your car. Has a Check Engine Light come on or what was the code stored that prompted replacing the ignition components?
If it ran good after components were replaced ensure wiring connections or vacuum hoses have not fallen of in the engine compartment. So many things could be responsible for making the engine run poorly it is hard to speculate without being able to drive the vehicle or perform some tests first hand.