I now have 3 kids, and we fly quite a bit. Unfortunatly most of the time I'm by myself with the kids. Just know it won't be that bad!! You are bound to run into some rude people, but just ignore them, or it might get to you. And when your little one is actually good on the flight then it'll be them that feels dumb.
As mentioned, make sure to have her sucking on SOMETHING during take off and landing. Otherwise it could be pretty painful. My kids at that age always seemed to fall asleep on the planes. They just lulled them right out. If it doesn't, just make sure to have toys to play with. I always try to bring something new they haven't seen before, just to keep them interested a little bit longer.
If you girl will watch any type of video or listen to music on the ipod, it doesn't hurt to have that handy just in case.
Bring those extra diapers, clothes, wipes and bottles (even if nursing) because you never know what they will do, or if the airline is going to leave you delayed sitting in that plane for a while.
Thursdays as the least traveled day, so if you can leave then, do it. It will make it easier. And the earlier in the morning the better. I found it doesn't matter when your kids naptime is, they are going to fall asleep or stay awake no matter what. They are in a new siutation, so that won't help. I actually like to take the red eye, so it is over bed time, and usually the flights are pretty empty (atleast that used to be the case, but who knows now days). I could even lay the baby down on the seat next to me to sleep most times. It was wonderful.
MUST DO: if your husband is traveling with you book an isle and window seat on the same row. That seat in between you is going to be one of the last ones taken, and if for some reason it fills up, you can check at the gate to see if there are any empty seats. If there are they will usually move that person in the middle to another seat. If not, you know that person is going to switch you to have you sit in the middle. They won't want to be there! It's worked every time for us.. but one. ;)
Definitely take the stroller, you'll want it. And check with the car seat/baggage now; some airlines aren't allowing that without a charge, and others are. You can ask about gate checking it (if regular checking isn't free, they may allow this which would be free). If there happens to be an extra seat and you were going to gate check the car seat, you can just take the car seat on with you and put her in that. That is actually the easiest way, since they know the car seat means they are buckled in and "Stuck" they don't get as whiny. Either that or fork out for another ticket for her. But I wouldn't do that with prices right now.
Layover or not is up to you. How does your little one travel in the car? I would rather drive, because then if my kid breaks down, it's just the person driving to has to tolerate it. Otherwise it's the whole plane. But on the other hand, that second flight is going to be so short it shouldn't be that big of a deal. So you'll just have to think about how good your little one is in the car!
I think that about takes care of it. Good luck. And remember, they can feel your stress, so if you stay calm.. chances are so will they!