Hi, Megan! I'm so sorry about your daughter's leg. I know you are anticipating it putting a damper on the whole trip, but it certainly doesn't have to.
The first thing to do is familiarize yourself with
Walt Disney World Services for Guests with Disabilities. My own daughter was booted for a trip we took this past spring, and I found it to be very thorough with the information and advice. There are attractions where you will be able to just get right into the regular queue with your daughter in her wheelchair, then others that utilize auxilliary entrances. You can also ask for a return time, if your daughter is uncomfortable waiting in line. This is part of the
Disability Access Service.
Wheelchairs are available at all of the
Walt Disney World theme parks, and at
Disney Springs, and there are even courtesy wheelchairs that you can borrow to get from the parking lot at the theme parks to the wheelchair rental locations. It is $12 per day to rent the wheelchairs, or you can rent one for the length of your stay, transferable between parks. Walt Disney World also has featured providers who can deliver a wheelchair to your resort and pick it up when you leave.
You'll find wheelchair accessibility extends to the monorails, buses, and boats. There may be an instance where there is not room to accommodate the number of wheelchair guests waiting in line for Disney transportation, but the wait for the next bus or boat is usually only a matter of minutes.
Have a wonderful vacation, Megan!