I believe if you are staying at GKTW, they offer Universal passes and Seaworld passes? Some of the posters on this board that have stayed at GKTW for their MAW trip could probably tell you more in depth on that.
My dd was granted her MAW trip and we went last June. We opted into not staying at GKTW, but at a deluxe resort on property. I did ask my dd's wish granter if it was possible we can get passes to IOA instead of Universal. He said it was fine and we did do IOA one of our days. The day we went to IOA, we only stayed 2hrs. at the most because of our time restrictions( we had to board our plane to leave for home that afternoon). The only area of rides we went on was the Dr. Suess/ Suess Landing area. Unfortunately, I don't remember about kids in wheelchairs and rides there.My dd does not use a wheelchair at all. I'm guessing in the Suess Landing ride area, the CMs should accomodate your son well. The CMs at Universal and IOA seem to be familiar with MAW families.
Also, both Universal and IOA have their own GAC cards. You just pick it up at Guest Relations at either park.
You should also be aware that IOA is a separate entrance from Universal. There is a ton of walking just to get to the entrance to IOA because from the parking lot, there is a lot of walking, then you walk by some of the restaurants, then you walk by the entrance to Universal, then you have to cross over CityWalk ( more restaurants and stores), then at the end of all that is the entrance to IOA. We didn't realize how much walking was involved to get to IOA until we got there!
Hope this helps somewhat. Have a great MAW trip!
Roseprincess