The dark rides in Fantasyland are good "starter" rides for those with fears or motion sickness. I don't think I would start with Spaceship Earth as some have recommended because it seems longer to me than say, Peter Pan and if he can't take the dark or whatever he will be traumatized longer (and so will everyone else in there with you if he is a screamer).
I can't recommend Tom Sawyers Island highly enough. My ds has LOVED this place since he was tiny and he still loves it at the age of 12. You take a raft over to the island, which opens at 10:00. If you are some of the first people over to the island you may find a paintbrush prop that the cms hide (not very well) for kids to find. You turn the paintbrush in for a certificate which is usually good for a fastpass to Splash Mountain or BTMRR. If you tell the cm you won't be doing those I'm sure he can come up with some other prize. If your planning on bringing snacks this is a great place to sit down, unwind and hand out the juice boxes etc.
There is a shooting gallery in Frontierland which all small boys should love. It does cost extra, but if he is having a rough time I'm sure this would brighten his day.
In Adventureland there are remote controlled boats that also cost extra, but are great fun. Another thing to do in this land is the Swiss Family Robinson tree house where you climb up a LONG staircase to see the replicas of the family's home from the movie. This is another of my ds's favorites.
If he did well in Fantasyland you could try the Jungle Boat ride here as well. It is very slow and the only dark part is when it goes through a cave.
In Epcot there is Innoventions. This is two buildings across from each other that have alot of interactive exhibits. You and your ds could spend alot of time here and have a blast! In the world showcase you could do the Kidcot stops as has been mentioned. My ds has always really liked the world showcase unlike alot of kids I've heard of.

If your ds isn't into it you can always try "candy around the world" that should get his attention

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My best tips would be to get the old Disney movies that many of the rides were based on and let him watch them. The Swiss Family Robinson is a favorite at our house. The original Tom Sawyer, maybe? We haven't seen this but ds read the book (as have we of course

). My ds read the book Johnny Tremain which was made into a Disney movie (which we also haven't seen, we're bookish people I guess) and alot of the themeing in Liberty Square is based on this movie/book. Ds was pointing out the Liberty tree etc to me last time we went, here's a way to sneak in a little education on them.