As a family of 5, we have had to split up on the following rides:
Goofy's Barnstormer (now The Great Goofini) - only 2 per seat were allowed
Expedition Everest - only 2 seats per row
Astro Orbiter - I have seen one adult with two young children, but when I went on with an 11 and 7 year old we had to split up. And, rightly so; we would have been uncomfortable. My 11 year old had his own rocket; your 9 year old could do the same if the comfort level is there.
Dumbo - same as Astro Orbiter
Aladdin and Triceratop spin (in the same vehicle, just not the same seat), not sure if this is always the case or because the 11 year old was willing to sit by himself
Speedway - I am guessing that your 9 year old would be tall enough to ride alone. Mine loved when they were big enough to go on this one by themselves.
Other potential issues:
Buzz/ Toy Story - fit 3 but only 2 guns.
Rock 'n' Roller Coaster is only 2 across.
Space Mountain is everyone sitting by themselves (one if front of another).
A few that 3 fit fine on that you might not expect:
Splash Mountain, BTMRR, Peter Pan, Haunted Mansion
If your 9 year old wants to ride any of the thrill rides, but the 7 year old doesn't, you could always go through the line together and then meet your oldest at the exit to the ride. Almost all of them dump into gift shops. Just be sure to be very clear about what he should do if he doesn't see you. It can be helpful to check out the exit first.
You may want to think about what the best way to do meals is. Buffets may be too much of a challenge, I don't know.
You mentioned a stroller for the 7 year old which may be a good idea. That way you don't have to worry about an escapee and you and your 9 year old won't become pack mules which can wear on you.
While I did not have the added challenge of traveling with an autistic child, I have traveled to Disney alone with the kids and in some ways it was easier than I expected. Without anyone else along, we could just go at our own pace and didn't have to take others' opinions into consideration. I've traveled with large groups to Disney as well, and while that is great in it's own way, when you are the only chief you've got nobody to debate with over the decisions.