Bummer!
I worry about that too. It was done under warranty at 10,000 miles (has just under 17,000 now) so I'm hoping I won't have to worry about it for a while, but I have the parts in my garage waiting.
One thing to note - I've established a really good relationship with my local Lincoln dealer (they do BMW and Mercedes too, so it's not shabby by any means) and they cut me breaks if I'm willing to leave it with them for a bit. For example, I had a full Mobil 1 trans flush with pan drop and filter change, 4 tire mount/balance (bought a set of Michelins from Tirerack), alignment, fuel filter change, recharge of a/c (car has pretty much sat garaged since 2002, so it was low on refrigerant and the compressor was cycling excessively), state inspection and a few other odds and ends (recall was done too, for free of course) for a few hundred bucks. I told them they can keep it as long as they want -- provided it's not left outside (I checked several times, it was always inside.) So, they worked on it when the techs weren't busy with customer waits and other "need it now" orders. I also asked them how much they'd charge to do the dreaded blend door if it ever happens... the service manager said $350-400 if I didn't mind being patient.
Just a thought -- check around, be extra nice... and deal with the service manager directly, not an advisor.
Not all of them are stealerships!
Good luck; hope you get it fixed quickly and on the cheap.