*UPDATED BELOW with pictures of the offending heads*
I hope it's not poor form here to post a major repair issue as a first post. If so, just yell at me and I'll be on my way.
Anyway, here's a summary of what I'm dealing with. I have a 2008 WRX with ~ 85,000 miles on it and no major issues to this point. In early November, the check engine light came on, along with the traction control light, and a blinking cruise control light (I'm told this means the car went into "limp mode"). I took it in to the dealer nearby for an oil change that was due anyway, and to investigate the CEL. They said the code was a missfire in cylinder 1, but tried a few things and claimed it was a non-issue. A week later, I left town for three weeks. After I got back, the CEL came back on within about a week. During the few days that I drove it with the CEL on, I noticed it idling rough a couple times. I took it back to the same dealership, and this time they confirmed that it is on occasional missfire in cylinder 1, and tried several quick fixes like swapping around coil packs, but the issue remained. At that point (this past Monday, the 17th) they said they needed to do a tear down and test the heads to find the issue. I was in a bit of a logistical bind at that point, and made the (probably incorrect) decision to let them do so, for the quoted price of $2900.
They have now taken all that **** apart, and say that both heads need to be replaced, along with all the valves and a whole mess of other things, for $4500 on top of the $2900 I already owe them just for the tear-down.
The main issue is apparently that the valve seats are burned out, but they didn't detail what's wrong with the heads. They also claim the clutch is in "very bad" shape, but I find that hard to believe, as I've never had it slip or feel unusual. It's certainly possible, but I've driven cars with a worn clutch, and this has never felt anywhere close to that. Regardless, the clutch isn't the major cost in all this as you can see below. I did have this same dealer do the most recent major service (was a late 60k) back in October 2011, and none of these issues came up then.
Posted below is the tech write up and invoice they sent me for the work they'd like to do. I made an attempt to anonymize it since I'm not sure it's appropriate to call out the dealer here just yet. I realize it's tough to judge what's needed without seeing the car, but this is a ****load of cash they want.
An additional complication is that the independent mechanics that I trust are located ~100 miles away from where the car currently sits, engine half-dissembled. I don't know of any reputable places near by that would be within towing distance. And they are going to want another $512 for gaskets and oil to put the car back together if I decide to drive it to another shop far away. So if the further shop is a significantly better deal, it may be worth getting it towed to save on that fee and save on labor at the second shop.
So I guess the main question I have is this, is it reasonable that a missfire in cylinder 1 could require replacing:
BOTH L & R heads
ALL intake and exhaust valves
Oh yeah, and apparently there's another rats nest somewhere down there. I had a problem with rats in the engine compartment about 2 years ago (there were rat pellets all over and they chewed through some wiring), but have since moved so it's obnoxious that they've somehow come back.
That was a really depressing first post, sorry.