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Whenever I buy a car I usually go through and change plugs, wires, (coil while you are at it), fuel filter, air filter, flush tranny oil, flush radiator and oil change. This ensures it is up to par. Your problem might not be related to any of these. Running bad leads me to believe it might be your plug wires arching. When it acts up open hood (night time is better) and look at both sides of the engine. If arching you will see and hear it. You might also need to replace one of your mounts (tranny, motor) but that would not make it run bad. Give more details...high rpm's, low rpm's, all throughout powerband. Does it knock while running in park or neutral? Is it almost like a 7 cyl feeling?
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