Update: So I changed the plugs Tuesday night (what a pain!) and swapped the coil packs from cylinders 1 & 4, figuring if it was a coil pack the misfire should move to #1. I also put Lucas fuel injector cleaner in the tank. The car ran okay during my ten minute test drive at 1am, but the check engine light came on again yesterday when I was driving from work to the gym (only about 1 mile) while the engine was still very cold (it's been in the teens here in Philadelphia for the past 5 or so days).
I pulled the code and now I've got misfires on cylinders 2 & 4. It idles low and rough when I'm at a stop, but when I'm moving everything seems normal, so far as I can tell.
I'm taking it back to the transmission guy today and asking him to take another look to make sure everything got hooked back up properly when they put the new clutch in last week. If they don't find anything, I'll be out of ideas, except to take it to the dealer and throw myself at their mercy. Unless any of you have ideas.
I would think if I had a valve or fuel injector problem, I wouldn't suddenly have 2 cylinders misfiring now. The transmission guy suggested that it sometimes takes a while for Subarus to readjust to the proper fuel mixture after having the battery disconnected. But it seems to me that a rough idle is one thing--multiple cylinders misfiring is another.