Totally different reason, but I have the same situation. I shattered my right leg last August, and so I am still rebuilding the muscles in my right leg and that leg is also about 1/4 inch shorter than the left. I don't notice the length difference, but the muscle atrophy & need for arch supports make a huge difference in buying shoes. Not to mention I also have what I refer to as "duck feet," much like you describe your daughters- where the heel is more narrow than the toes.
So... for the heel/toe box difference, you can get heel inserts for your shoes. I just get mine at Walmart- they are just foam pads that are molded to fit into the heel of your shoe and helps with the slipping of the shoes over the heel which causes blisters.
As for the arch supports- I also get these from Walmart- Dr Scholls makes ladies sizes which can be cut to fit. I also got a pair this last time which has adjustable arch supports. Some days I don't feel I need as much support, so I wear the weaker ones. but for your daughter, you could possibly put one of the firmer ones in one shoe, and a lighter one in the other. Just be sure to get shoes that are fairly open at the top if the top of her foot raises rather high like mine does naturally. I've lived the past few months in those shoes that are designed kinda like tennies, but are open on the top similar to ballet flats. With the arch supports, they are comfortable, give me room for my supports, and are flat- which is still a must as my ankle isn't strong enough yet to wear anything different.
On to that issue- Most people don't notice the difference in my legs either, unless they know the story. I've spent almost an entire year healing from this awful break (no surgery, thank God!), and unless they know, people can't tell. BUT I can certainly tell the difference and am still slightly self-concious about it. Not to mention that it makes everyday things difficult. My Ortho has me doing different excercises to work the muscles- one of hte main ones is bike riding. Another to strengthen just one leg at a time is single leg presses- she would stand on one foot (or just shift her weight to it to begin with, using the other for balance) and stand up to her tip toes. Walking on the backs of your heals help keep from getting chin splints by working the rear muscles & not the front.
My ortho is fantastic!! I can't recommend him enough...
Dr. Carl Cannon of the Woodlands Sports Medicine Center ###-###-####. His staff is amazing also! I will forever be known there as "Captain Morgan" because of the long cast I was in... But every time I call in with questions, they are fantastic! I haven't had to take my little one in to see them, but over the 9 months I was constantly in there, I saw lots of kiddos there for treatment.
Sorry for all the rambling, but I figure if I can help someone else with my experiences, then it's good for something! =o)
Feel free to send me a personal message if you'd like to discuss further.