Hi Amanda,
I think you're really going to like traveling to Walt Disney World at this time of year! The crowds should be much lighter, you get to take advantage of free dining, it's during
Epcot's Food & Wine Festival, and you'll get to go to Mickey's Not So Scary Halloween Party. Plus, traveling with 2 adults, rather than an entire group makes getting dining reservations a bit easier as well.
The 29th is the Twilight Zone Tower of Terror 10-Miler race. You might find that the weekend is a bit crowded. I would avoid Hollywood Studios on Saturday, September 29th. Also, during the Food & Wine Festival, I find that Epcot tends to be a bit more crowded on weekends with locals visiting the park on their day off. During the week, you should experience light crowds at any of the 4 parks you go to. You'll find the parks getting more crowded on the last couple days of your vacation because of the Columbus Day weekend, but, overall, you'll see much lighter crowds than you did in May at the beginning of your trip.