We have had very heavy rains since yesterday and when I left the house this morning in the dark, I ran into a very deep area of water only 2 blocks from our house. The car stalled and so I left it there.
I'm worried that with the FWI, water may have gotten into the engine. Other than pulling the plugs, changing the oil and possibly the transmission fluid, any other suggestions or recommendations?

I decided to have it towed just in case there is any internal damage, thinking being that the mechanic can give State Farm an unbiased opinion. When I was able to get to the car in the daylight, the front air dam had been ripped off(I was only going about 25mph) and the carpeting was soaked but at least there wasn't any actual standing water inside.

Thank you very much for the tip on inspecting the rack. That was one I hadn't thought of. I take it your starter was none the worse for the wear.

I count myself very lucky in that there was no damage to the engine even though it was full of water. Once it died, I didn't try to restart it which is what probably prevented any damage. State Farm is authorizing new carpeting and pad so if there is a positive to all of this, that would be it.
The mechanic had pulled the plugs the other night and when I went in to talk to him, we looked at the plugs and they were like new although they had 40,000 miles on them. I never gave it a thought that he would go ahead on his own and replace them although he did say they were soaked. At any rate, when I picked the car up this morning, he had gone ahead and replaced them and the State Farm adjuster was ok with them picking up the cost for it. However, I asked the mechanic what plugs he put in and they were the factory platinums which, since I have a 3.4" pulley, means those have to come out and be replaced. Oh well, so much for the free plug change.
Just a reminder to those with a FWI. Never try to plow through standing water or you could be a whole lot less fortunate than I wound up being.