Ok, couple of points here.
First, invest the money and purchase a Sit-N-Stroll Stroller when traveling with a little person who 1) needs a stroller and 2) needs a car seat.
http://www.strolex.com/
My son is only 22 months old, but have taken eight seperate airline-based vacations, including a month's vacation in Europe. We bought this after doing research and can tell you it is a heck of a lot better than using a traditional stroller in the airports. The seat is FAA approved, fits down the aisle of airlines, serves as his seat on the plane, and, when we arrive at our destination, serves as his car seat.
I do, however, recommend having a seperate, "more comfortable" stroller with you that you check as luggage. The sit-n-stroll, although great for airports and short jaunts, doesn't serve well being used as the ONLY stroller on long trips. Check out the link above and you will see what I mean.
Regarding your seats in an exit row, check with the specific airline. I'm pretty sure that seat restrictions are only for the window seats right next to the exit door.
Even if you use a brokerage house (expedia) to book airline seats, after your tickets are issued, contact the airline directly and request seat assignments. However, the airlines can change them on you without consulting you beforehand.:-(