Andy that is really unfortunate, and I would even suggest pulling up the carpeting to get the underside dry. I know that will be a major PITA, but otherwise mold might form like Hank said. As far as your engine is concerned, well, if nothing has seemed wrong so far, it should be ok, hopefully you were not accelerating while going through the deep water. Otherwise any water that got into the intake tract, etc., should be dried up by now.
I also ran through a very unexpected large pool of water a couple weeks ago (it was one of those flash floods here in TX), and I seriously hit this water fast. I instantly took my foot of the gas pedal and just steered through it. I hit the water hard enough that the two front fender liners popped out of place, and my fog light cover got knocked out of place. I also notice where water entered into the intake, but never made it to the engine.
Anyway, best of luck to you!