Lynn,
This is not as much of a mess as you think. You have scheduled some great meals, and that is a significant part of an overall good time at Walt Disney World. Here is what I would do for a daily schedule, assuming no park hopper;
- September 29 - No park. Enjoy your resort, take your time settling in, and plan time to explore the Animal Kingdom Lodge before your dinner at Boma.
- September 30 - Epcot
- October 1 - Magic Kingdom
- October 2 - Hollywood Studios
- October 3 - Animal Kingdom
- October 4 - Hollywood Studios
- October 5 - Epcot
- October 6 - Magic Kingdom
The October Extra Magic Hours have not yet been scheduled, so it is hard to say if you are making the best use of them. But consider them a nice plus if they hit on your park days, and don't feel like you have to chase them.
As for breakfasts vs. dinners, that is really your call. I like having nice table service dinners like the ones you selected every night so that we can be entertained, and so we can talk about the day that has just passed.
Ask more questions, and am glad to help!
Have a magical vacation!