Have you checked all the ignition components? With the rough idle I'd suspect the spark plug connectors,but check the coils themselves also. I've seen coils crack around where the connectors attatch and cause a cylinder to miss. If it's running bad enough, you may be getting on the throttle enough to fool the computer into thinking you're just driving fast. There shouldn't be many opportunities for a vacuum leak on your engine, but it might not hurt to check for that. Another possibility is the mass airflow sensor. When they go bad they can cause all sorts of driveability problems. As for the valve body, about the only thing that causes problems there is the conductor plate. I haven't seen too many bad shift solenoids. Usually if it's going bad it will go to the limp home mode and leave you driving in low gear. Hope I gave you enough ideas to get you started.