It sounds like you have about a year and 8 months before your trip. With this being a new diagnosis, her being so young, and the trip still being a good ways off, try not to stress yourself out too much as it's hard to know how she will be over a year and a half from now. Strategies for helping to make things easier for her will largely depend on what difficulties she is having (which again, it's hard to necessarily know how things will change between now and your trip).
Just some general tips though:
I second the idea of getting the stroller as wheelchair tag if she has anxiety in crowds as it will allow the stroller to be brought in ride queues and give her a space of her own. Bring along a small lightweight sheet/blanket to drape over the canopy of the stroller to help fully enclose it to block out outside stimuli. You might also consider bringing a stroller fan to help keep her cool as September can get hot and being uncomfortable can help to trigger anxiety for many people.
In line with keeping her comfortable, sticking to regular meal times and drinking plenty of fluids is very important. It can be easy to get off schedule with things like that at Disney. Straws and lids are difficult to find in the parks so you may want to bring a favorite sippy cup or two to transfer any drinks for her into. Also, some favorite snacks brought from home might bring comfort.
Closer to the trip, you can show her videos of the parks to get her more familiar with them. Videos of meet and greets, ride POVs, and of the parks in general. If there are local amusement parks near you (or even something like a zoo), it might help to take her there to get her more used to being around lots of people, lines, etc.
There are several areas throughout the parks that tend to be less crowded and are good if she needs to get away from the chaos for a bit. The animal trails in AK and Tom Sawyer's Island in MK immediately come to mind.
If you are flying, many airports offer a program for kids with special needs to allow them to come on a different day and go through the airport procedures to become comfortable with the process before your flight. TSA Cares can also assist passengers with special needs when you do go to the airport for your flight. Make sure to call and ask for that assistance at least 72 hours in advance.
Work with her doctors/specialists to try to determine if there are specific triggers for her anxiety and what, if anything, helps to calm her. My son had bad anxiety when he was a baby and toddler (he's 4 now and thankfully his anxiety has significantly improved) and grocery stores were incredibly difficult for us as well. The one thing that really helped him was looking up at the ceiling. It sounds strange, but when he would start to meltdown, if we could get his attention focused on the ceiling, he would start to calm down. The doctor thought it may have been that he felt like strangers were closing in on him and looking up at the ceilings helped him to focus his attention elsewhere and not feel so closed in since the ceilings were so tall. That same strategy actually helped us in several lines at Disney when we took him at 2 as there were often interesting light fixtures or pipes in the ride queue ceilings that could draw his attention away from the people surrounding him.
Distraction techniques can be very helpful with redirecting focus on to something else. My son enjoyed looking for hidden mickeys around the parks and playing simple games of iSpy (do you see something red?) and it helped to give him something else to focus on when he was uncomfortable.
Definitely take things at her pace. Be willing to change plans if she needs a break or doesn't want to do something at the last second. Saratoga is a great resort for relaxing and walking around. It's where we stayed as well on that trip when our son was 2. It's very peaceful and there are loads of areas to walk around and get away from people. The 2 feature pools are a lot of fun with slides for little ones (the one in Paddock actually has a separate kids water play structure with slides and fountains). There are also quiet pools in Grandstand and Congress Park which are typically far less crowded and may be a good choice for some relaxed fun without as many people.
Also for the hotel, consider bringing her favorite blanket, stuffed animal, and maybe even pillowcase from home as it may aid in making her feel more comfortable sleeping. I mention pillowcase as smells can often trigger feelings of uncomfortability and her own pillowcase from home will smell like your laundry detergent which is what she is used to smelling when she goes to bed at home.
Good luck! I hope her anxiety improves as time goes on.
