2006 - Misfire, Flashing Cruise/CEL and code P0303?

I have a 2006 Forester that I got used a year ago. After a head gasket repair job, it started a week or so later with the cruise control not working, and both the Cruise light flashing and Check Engine Light being constantly on. The mechanic read the code (P0303) and wasn't sure what exactly it was. It wasn't doing any actual symptoms at that time, so it was reset and we just let it slide. It was back to being on within days. I figured if that mechanic didn't know for sure, I would try the dealer. So after $700, I have new spark plugs and a cleaned throttle body. And it ran smooth - for a week. Now it's back to it again. It does actually stutter a bit on accelerations now, so the misfire warning seems likely. Something on-line mentioned potential causes as being: fuel injection, spark plugs, wiring, and coils. The non-dealer mechanic at least mentioned wiring and coils to me, but didn't want to throw away my money on a trial and error thing if it wasn't having any actual symptoms (at the time). I was wondering if this rang a bell with anyone out there and if so, what was the cause? I'm going to limp along with it for a while and see what happens.