Hopefully the water wasn't as deep as seen on the YouTube Channel, Rufford Ford, Vehicles vs Deep Water.
Honestly, any car older than 8 or so years, that has seen it's share of proper Winters and Summers, should NOT assume the electrical connector seals are still water-proof.
As you have found out, driving your car in the rain (even heavy rain) is NOT the same a water immersion.
Your best bet is to allow your vehicle to drain/dry (in a garage?), then run ISTA, clear the codes, then start working each "hard" fault one-at-a-time.
Let us know how you fair....
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