We will likely be going on a Sunday in September. Figured all parks we are going to (Sea world, universal, island of adventure, MK and Blizzard beach) will all be busier on the weekends, so migh as well go to sea world as it is mostly shows that hold a lot of people.
We are rope drop people and plan on riding atlantis first, and then heading to the kiddie rides section, as those will probably get busy later. Then after that we will stick to the shows and exhibits. Likely won't ride the bigger roller coasters.
Anything I'm missing that we should hit early before the crowds swarm in?
Well which Sunday in September are you going to Seaworld? If it's any Sunday except the 4th, then crowd size won't be an issue at all. September, next to January is the slowest month of the year. Even on weekends. The park may get 8,000-10,000 people and that's nothing at all. So I don't think you will have to worry about crowd size (Except for the 4th which is labor day weekend and usually extremely busy)
As far as a touring plan, I would plan your day around shows. Decide which shows you want to see and plan on visiting exhibits/shops/restaurants around the show stadium before and after the show time. For example, if there is a 2:15 Sealion show that you want to see, then visit exhibits around the Sealion show stadium from 1:00-2:00 and 3:00-4:00. That way, your not running all over the park. In the ideas you mentioned above, you want to visit Journey to Atlantis and then the kiddie area (Shamu's Happy Harbor). Journey to Atlantis and Happy Harbor are on complete opposite sides of the park. So you will be walking from one side to the other and then back again to see any shows or exhibits you missed.
Show times for September should be posted later this month. The show times on the Seaworld Orlando site now are wrong. Those are the San Diego Seaworld's shows. It's a technical glitch. I would get to the park at park opening (9:00) and do the following in this order: Go see the Flamingos, turtles, and sting rays. Then the dolphin feeding at 9:30. Then I can almost guarantee there will be a 10:00 Blue Horizons Dolphin show. So that would be next. Followed by Journey To Atlantis, Penguins, Sealion Pool, Sealion show, Lunch, Pets Ahoy Dog and Cat show, Shark Exhibit, Shamus Happy Harbor, Shamu show, Wild Arctic (Ride and Beluga whale, walrus and polar bear exhibit) and then on your way back to the front of the park see the dolphin nursery on your way out.
Again, that's just my suggestion to save you time. Plan your day the way you want to but most of all I hope you have a ton of fun and make a lot of new memories!!!!