Our daughter also has CP and uses a power chair. She and I used Magical Express in May. As Carol said, be sure to tell them when you make your reservation.
However, when we got to the ME counter, the agent said she would need to alert ME that we needed a bus with a lift. I told her that we had alerted ME to that fact when we made the reservation but she said it didn't matter. We would have to wait until they could get a bus with a lift.

Now this lady was NOT a typical WDW CM. Frankly she was a pill so I did take everything she said with a grain of salt.
Anyway, we waited for just five minutes or so before being directed to a bus with a lift. Unfortunately, the driver had trouble with the lift. We did eventually make it to our resort.

But this was in May and ME was brand new. I suspect the drivers are used to the lifts by now. I did read that most of the ME buses have lifts.
The buses and therefore lifts are very high. I don't know the proper bus term but think luxury buses. This freaked me out but she was fine. Like you, she deals with harder challenges on a daily basis.
So bottom line, let them know ahead of time and I bet you'll have a good experience. After ours, my daughter was reluctant to use ME again but I've convinced her that it should be fine and we are using it again next trip. I hope I'm right!