I think if it were my pool in your situation, I would strongly consider changing out the sand in the filter once you get the pool cleaned up. Normally sand doesn't really need to be changed, but my personal experiences with the stuff that was in the floodwaters down there lead me to believe that you need to be rid of all of it to truly get your pool clean.
I agree with the others...rake out what you can, bleach it, maintaining 10-15 ppm all the time, and vaccuum and brush as the water clears so you can get to as much of the debris as possible. Use a drop-based test kit for testing, so you have accurate numbers to work with.
Good luck!!
Janet
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