Good morning, OP here with a followup/resolution. I took my car to another Ford dealer and they retrieved the code that caused the check engine light to come on. Long story short the #6 cylinder was misfiring, so they recommended replacing the ignition coil and getting a tune up that included replacing the spark plugs. This problem was unrelated to the flooded waters I drove through.
As for my flood damage concerns, aside from having the flex pipe repaired, Ford recommended servicing the trans fluid (flush), rear axle service, and power steering (flush). Oh and of course, my battery (over six years old) didn't pass the battery check test so I had that replaced as well.
Just a quick thanks to all of you who provided their recommendations. When it comes to cars, I'm not mechanically savvy and sometimes it's difficult knowing what questions to ask.
