Mitsubishi Repair: 1999 Mittsubish Galant- engine running rough, valve cover gasket, mitsubish

Question
I have a 1999 Mitsubish Galant ES 3.0, automatic and when I start the thing, the engine runs rough.  And when I shut if off it makes this hissing noise.  I just recently had a tune up (spark plugs, wires) They are still waiting on the cap and rotor the old ones are still on.  I also just had an a/c comppressor and a/c clutch put on because the old one went out.  My valve cover gasket has been leaking so I got that replaced. It sounds a little better but it still runs rough.  I have 122,000 miles on it. If I get the new cap and rotor put on and the transmission flushed (cause I have never gotten it done) Ive had the car for almost 3 years.  Will it stop running rough or do you think the problem is something else.  

Answer
Michelle,
Your rough idle may definitely be caused by your old distributor cap and rotor.  Getting your transmission flushed is also a very good idea.  It should be flushed every 40,000 miles, so you're well overdue for that.  

Hopefully replacing the cap and rotor will cure your rough idle; it usually does if your cap and rotor are really worn.  You may want to also get your air filter and fuel filter replaced if they weren't replaced in your initial tune-up.  
Good luck!