Welcome to the RTA forum!

Your basic outline is good, and your cost estimates seem to be in the ballpark, however there are a couple things you should know.

First, your 3 weeks is going to fly by faster than you think. It will be enough time, but you're looking at at least a full week just to drive the route you are talking about, so a couple days here and a couple days there will start to add up quickly.

A couple things with the specifics.
First, the Kennedy Space Center is along Florida's east coast (near Daytona) and that's where they actually launch the shuttle. The Johnson Space Center is in Houston. I'm sure either one could be a fun stop for your family. I haven't been to Houston myself, but I could see this as being a nice place to break up the trip.

Seaworld also isn't located in San Francisco, the one in California is located in San Diego and so it wouldn't be on your current route. Personally, I wasn't too impressed with Seaworld when I went to the Orlando location last year. What I would recommend instead is to stop at the Monterey Aquarium as you are traveling up the California Coast. You won't get the dancing animal shows that you get with SeaWorld, but you'll get a more authentic experience seeing marine life.

For flights, I'd probably see if you get get a good price on a flight from SFO that's with the same airline that you'll be connecting to central america. If for some reason you'd have a problem or delay getting to your connection and your flight is on the same ticket, then the airline is responsible for make sure you get to your destination. If you take 2 airlines, you wouldn't have much help if you miss your second flight because of a problem with the first. At the very least, you'd want to give yourself a full day between connections just in case.