I also read over the TSA's web page for travelling with children which includes an informative section on travelling with medications or mobility aids. http://www.tsa.gov/traveler-information/traveling-children. Following some really good advice I called and expressed my concerns to the TSA contact office http://www.tsa.gov/contact. They helped me get the number for my local airports TSA office. I contacted the local airport office and got a lot of helpful specific airport advice that really streamlined our travel experience. All in all I found the TSA incredibly helpful. They helped make both our trip to and from Boston an overwhelmingly positive experience.
I was pretty paranoid regarding germs during our travels so we brought sanitizing wipes on the trip. My husband would board during the special needs boarding. He would wipe down the walls, windows, trays, seats etc. and then install my son's car seat. We would then board last and I was able to put him in the car seat with no problem and minimal worry. The flight out was a non-stop flight and went flawlessly. The flight back was in 2 segments and we had a couple of serious diaper leak problems. Our son was on lasix, it took quite some time to find a way to diaper him without compression leaks with every urination. (The secret is Flip disposable inserts. Whether you use cloth or disposable, you need this boost when dealing with that dang lasix pee).
It was also strongly suggested that we ditch our very nice and SUPER HEAVY car seat and get a $40 cosco Scenera car seat instead. There is a lot of amazing information in this BabyCenter thread regarding travelling with a car seat: http://community.babycenter.com/post/a36576082/using_a_car_seat_post_open_heart_surgery
I found that clear explanations and sincere gratitude along with a wealth of patience, made for a mostly pleasant travel experience.