Thankfully, this isn't one of my steeds, but what is the best thing to do if an aluminum bike of recent (less than 5 years) make has been completely submerged in water for over a week, likely a month or so.

The only real suggestion I can think of (other than to take the thing to a LBS) is to use a penetrating oil in every major part (headset, stem, cranks, seatpost, drivetrain), disassemble, clean, grease/oil, and reassemble.