I just wanted to post a follow up report to my question from April after our 10-Day trip to WDW a couple week ago. The advice offered by Grace was spot on. We went to Epcot GR on day 1 and they were absolutely wonderful. They asked about my son's needs and without hesitation issued a 10-day Alternate entry GAC. (granted he made it easy by sitting in the corner with his headphones on playing his Nintendo DS).
The GAC was handled as advertised. On some attractions that had very long standby waits, the CM would ask who was the person on the card and ask my son if it was him. They were very nice to him, giving him high fives for the courage to go on the Rock n' Roller coaster and offering to have him make the announcement to move the queue(he was too freaked out to do that, but it was very kind of them) and their demeanor made him feel welcome. I was nervous about that ride with him (as was he), but after we rode he claimed it as his favorite and we rode twice more and he still talks about it. I would wait the 90 minutes, but there was no way he would have survived it. Thank you Disney for your accomodation of kids on the spectrum. It makes great memories possible that otherwise we couldn't even think about.
One final note. The friendliness and interaction of the CMs at the parks varied quite a bit. By far the most gracious CMs were at Epcot, followed by HS and AK, which were both really great as well. We were very dissapointed in the attitudes of the CMs at the Magic Kingdom. They were nearly all curt, grouchy and matter of fact. This shocked us since we thought MK should have been the most "magical" park, but we felt like we were at six flags based on the attitudes of the CMs there. We still had a great time, but it was a very noticeable difference (made me thankful we went to the GR at Epcot).
Thanks again and I encourage anyone who is nervous heading to WDW with their spectrum child to make sure you go to Guest Relations first. That card was a massive anxiety reliever.