While our situation is a little different due to her age -- I encourage you to go to guest services and see about getting a GAC to use in situations like Soarin -- ...........
We were able to get the GAC without a doctor's note, but I will have one with me for the next trip just in case. Maybe you can get a letter explaining you need to minimize standing times and use an alternative entrance.
You basically used the child equivalent of using a wheelchair - you were able to use a stroller as wheelchair.
For adults, the advice WDW would give would be to use a wheelchair or
ECV - which the user does not need a GAC (Guest Assistance Card) in order to have it in lines. That is the advice that Disney gives both in the parks and in their Guidebooks for Guests with Disabilities. There is more information about GACs in post #6 of the disABILITIES FAQs thread.
Quite a few people have posted in the past that they got a GAC that they thought would help them avoid standing, but because there are so many places where standing is part of the way the attraction is loaded, it was really not useful. They also found it did not shorten the distance they walked, so most of them opted to get a wheelchair or ECV on their next trip and found they had a much more pleasant experience. That's where the advice given was partially coming from.
Most attractions don't have alternate entrances, and for those that do, it may not shorten the time standing (an exception would be Spaceship Earth, which does have a nice waiting area with seats). But, we have waited in that area already for over 30 minutes when the regular line was basically loading as fast as people could walk.
Soarin is difficult for anyone with problems walking - someone measured it and it is over 1/4 mile to get from the entrance to the boarding area and after riding, you go the same distance to get back to the entrance (and that doesn't include the walk to get into the building in the first place. During the preshow, unless you have brought something to sit, you will be standing for at least a few minutes before and for the duration of the preshow.
One thing to keep in mind about Fastpasses is that everyone in your party does not have to be present to get one. You can send one member of your party ahead with all of your party's park passes and that person can put all the passes into the machine to get the Fastpasses. We frequently do that and it helps to avoid backtracking.
A lot of people have used the tour planning services, such as Tour Guide Mike
Also, to go along with this -- are you open to a walker? I know that there are some nifty ones out there that even have a bench/tray that you can sit on when you need to.
On a personal note --

-- as a mom, I often try to look ahead in the crystal ball and see where my daughter will be. That is the absolute b*tch about SBO. Not knowing when or where it will hit and how much it will degenerate. This week she will be getting an MRI to see what is going on with this pain that started at Soarin and is still going on now...
That is a good suggestion about the rolling walkers with seats (you can find them by searching for Rollators).
And

that you get some answers (and even better), some solutions to your DD's pain problem.