Could you guys list some of the causes for my cars symtoms?

Just doing a little troubleshooting. My 89 trooper has a rough idle difficult to time, lacks power and hesitates on acceleration. I will need to replace the throughout bearing and possably the clutch but I dont think that will affect the engine. The engine is the 2.6 4cyl model. If I where to take a wild guess I suspect the problem is in the ignition system. This is a project car and not my daily driver. I am mostly looking how to troubleshoot the car myself. Any opinion other then take it to the shop will be appreciated.