I think you are on the right track, like you mentioned start with the cap and rotor. Clean your MAF and throttle body, since it never hurts even if it isn't causing the trouble. Given the time since the last tune it might be time for some new plugs or at least an inspection and regap (if you are REALLY cheap, me, if I go through the headache to pull a plug, I'll replace it).
See what those things do for you, no fix, start checking things like the engine temp sensor, O2 sensor, testing for bad injectors, etc.