Hi Stephanie,
What you described - taking advantage of Extra Magic Hours in the morning and then park hopping - is what we do trip after trip; we believe this is one of the best strategies for avoiding crowds and lines. Often, we do stay at the first park through the morning to take advantage of some fast-passes, too.
During our transition to move to the other park, we usually take a break by having lunch or visiting the pool. Because a break is worked into the "transition," we don't think about any loss of time. The break also helps to keep all of us energized and refreshed. If you do move park to park, the transportation time is never too bad. It may help to plan the park hopping to move to those that are nearby each: Epcot and Magic Kingdom are connected by the monorail; Epcot and Disney's Hollywood Studios are connected by a boat ride and/or a short walk. The Animal Kingdom is nearest to both Epcot and Disney's Hollywood Studios.
Ahh, but with your visit in September, you may find that the crowds are smaller!
Have a magical trip! Kara