Everyone has pretty much answered your questions, I just wanted to throw in some dining preferences of my own.

Magic Kingdom - You picked all of my favorites, I'm sure you will have a great time.

Epcot -
Le Cellier (Canada) has WONDERFUL steak (if you like that sort of thing)
Japan - My daughter enjoyed this restaurant immensely because it's so visually stimulating, which would also be good for your toddler. They have a restaurant where they cook the food in front of you, they really involve the kids and it's fun to watch as well!
San Angel Inn (Mexico) - For nothing more than the atmosphere, the food is decent enough, I enjoyed the chicken tacos, it IS a little cramped though but you get to see the boats go by for Gran Fiesta Tour. I'm told it's like your Pirates at DL.

Hollywood Studios -
50's Prime Time Cafe - It's a great old style family atmosphere/food and it's great to see the wait staff yell at grown men to keep their elbows off the table.

Animal Kingdom -
Yak and Yeti - I've had nothing but great experiences here, food and atmosphere. However I've read some not so great reviews on this restaurant so it sounds like it's hit or miss.

Hotels
Ohana (Polynesian) - Great food, great atmosphere, great fun for the whole family. I mean really, who doesn't love a coconut race in the middle of dinner?
Boma (Animal Kingdom Lodge) - Breakfast is phenomenal and dinner is great if you love spicey food, it always gets rave reviews.

Have a great time!