I can't offer too much advice regarding special needs children, but I can pass on what I learned about flying. I recently flew with my 15 month old and I read lots of articles beforehand. My husband and I went ahead and purchased her a seat of her own, which helped tremendously. I think she thought she was on a car ride since she was in her car seat. Most airlines will offer a discount for young children.
It is recommended that you give your child two new toys on the plane. This way it is something new that will excite and distract him. Another thing I read is that you should board the plane as late as possible, even though they offer early boarding. It helps keep the child from being confined for so long.
Also check the airports for play areas where your son can climb and play during your long layovers.
I hope this info helps. Have a safe trip.