I don;t own a D2X, but I would certainly send it in.
It really sucks to have your new $5k tool spend more time in the shop than your hands (and when in your hands it has to be used for quality testing, whata bummer!), but man would I be super po'd if ANY focus sensor was mis aligned.
You might think it's cool to know which sensors FF or BF, until in a total time crunch you are trying to nail some shot of something in flight, and it goes into that sensor and your"keeper" becomes just another OOF shot on the scrap heap.
It would be interesting to know the actual numbers of people with these problems. All over the internet you see "I have 10 friends who have perfect d2x's" or "the people with problems are a small vocal sampling, not representative"or "the people with problems are inexperienced with a high resolution sensor"),
then here, in a community of limited size, I see one, two maybe 10+ people who know what they are doing as photographers, but still have several repairs or replacements on their d2x--- so ***?
Spot meter 1 stop off- this is a new one, but that totally sucks too.
I think you should not only send it in, but your note should specify that this is the second major repair, and further I think Nikon users should investigate the lemon law (I am no lawyer, but I Think with cars, if it needs to be repaired three times for the same thing you can demand a replacement) as a means to demand replacement cameras.
What I think is most disturbing are the hundreds (thousands, perhaps tens of thousands?) of D2X's owned by less skilled photogrtaphers, all who probably have no idea how to check sensors for FF or BF and have mis-aligned cameras resulting in lots of wasted shots.