Ok now listenup someone who has this problem on a 5sp unplug the brown plug at the transmission this is the nuetral safety switch. This will take it out of loop for ecm. drive the car at 60 to 70MPH in 4th or 5th (above 3500rpm) or adjust valves for 3to 4hrs and have the same problem.

After talking to the above poster, he's got a ton of experience on Subarus, and while the valves can cause a problem, it seems a lot easier to me to do the NSW fix first.