If you haven't already done a search on this forum, you should, because this topic comes up frequently. I'm not sure of the protocol for referring to other websites, so forgive me if I err, but I wrote a very detailed trip report for Brian Bennett's Mouseplanet on my first trip to WDW with my autistic son (Summer or August 2001 in the archives). Prepare to be amazed by your son's positive response to so much happy Disney stimulation! The pool break in the afternoon is always a great idea - for the whole family. Plus, I don't know of an autistic child who wasn't a water-baby. The GAC is a great help and we imposed our own limits on it, if only to teach our son that waiting in line is part of life. We never used it for posted waits of 15 minutes or less. Some new CMs still need to be educated about it but we kept a positive attitude and it went well. When you go to Guest Services to get the card, bring documentation from your son's doctor. Under the ADA, supposedly you don't have to "prove" a disability, but rather than get into a debate with the CM, just provide a letter from his neurologist stating his diagnosis and need for special consideration with regard to waiting in line.
We have gone 3 times in the past 2 years and each time our son has had a melt-down. However, it can be expected of many overtired, overstimulated children. Not a big deal.
Enjoy and watch your son's development leap!