Do you mind if I ask - if you're planning on being at FW for a week, why you're only going to those 2 parks, and each only for one day?
If you've got a schedule of lots of other non-Disney things to do, I can understand that. And if money's tight, I can understand that, too. Just curious.
The best advice I can give you is to not plan too much of a schedule in your situation - a 3 year old and an infant. You're not going to be a park commando this time. They're just going to need too much of your attention.
When at MK, take advantage of the early morning extra magic hour and hit Fantasyland (straight up and through - or around - the castle and behind it). Most of the rides a 3-year old can experience, and will want to experience, will be there, especially Dumbo which is a big deal for wee ones. Hit Dumbo, Teac Cups if your stomachs can stand it, and the traditional movie rides like Peter Pan & Pooh & snow White (a little scary for wee ones, be warned). Get a Fastpass for Philarmagic if you need to, then either go to Tomorrowland and ride Buzz Lightyear, OR go to Adventureland for the Jungle Cruise & the flying carpet ride (a spinning ride just like Dumbo, but with flying carpets and a "spitting" camel in the middle). I'd worry about recommending anything else without knowing what your 3-year old can handle.
As far ask AK goes, I'd suggest going at opening, BEFORE opening if you can. Since the EMH are at night, a lot of people will avoid going early, so the park might be as empty as the early morning EMH often are, except it'll get MUCH busier as the day progresses. Head straight for the Kilimanjaro Safari. Finding Nemo can get packed, so whatever the first show is, you're probably going to want to be on line for it at least 30 mins before the first show. So in-between Kilimanjaro Safaris & the first Nemo show, whatever time you have go through the walk-through animal exhibits, or the bird show. Other than that, again, without knowing what your kid can handle, I don't know if I'd recommend "It's Tough To be a Bug" and even if she could handle it, one of you will have to remain outside with the baby. It gets loud, people scream, it'll freak the infant out, more than likely.
Just take it nice and slow and understand your 3 year old could easily get overwhelmed, and prepare accordingly.