Well, a tune up may help. I would first check for vacuum leaks on and around the engine. If you do a tune up, make sure to replace the fuel filter too. It may still be the original one. As far as the transmission service, if the fluid is getting dirty, you should. But, I don't feel that has anything to do with the engine running rough. My first guess would be a vacuum leak.
Let me know what you find.
Friday, July 10th, 2009 AT 11:05 PM