I had the same problem, and it was a clogged (actually "kinked") sunroof drain hose. Mine was soaked just as you describe.

They ended up replacing the carpet and padding/insulation. If it makes you feel any better, all seems fine now - no musty odor or any residual issue. I don't recall them having to remove the console or seats - if they did, I couldn't tell when I got it back.

The only problem was getting the replacement carpet - it took weeks to come in, perhaps because I have the less popular tobacco color. Didn't bother me, my x5 is two years old and I was provided a real nice loaner. You may feel differently since you just took delivery. Good luck.

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2008 X5 4.8i, Jet Black, Tobacco Nevada leather & just about everything else (no vent. seats, no 3rd row)