I think the first two responses were great. I was shy when I was growing up - particularly at that age. It breaks my heart to hear about your son's struggles.
I wore these coke bottle glasses and did well in school. As you can imagine, I didn't really "fit in". I had several experiences similar to what happened to you and your son at McDonald's. Getting contacts when I was 13 certainly helped and by high school, my social situation improved because the pool of students was so much larger. By college, I made a lot of great friends and I would consider myself a social and happy adult. I have told you that so that you know that it won't necessarily always be this way.
I am so encouraged to hear that there are programs out there that help children with socialization now. My mom did not push me, she just let me be me and always told me that I was smart and special and that she loved me. She encouraged me that I would find friends I liked, it would just take time. She discouraged me from joining the mean girl group just to have "friends".
As far as marking him down on his grades, I think you need to have a discussion with the teacher, maybe even the principal, and the special ed teacher as suggested. My fear would be that it could discourage him academically as well. Since he does feel left out socially, he needs something to help him feel successful. If school and grades are his things, and he is getting marked down for participation, I don't think that is fair. I'm sure elementary school education has changed a lot in the past 20+ years, so maybe I am out of line. I am just speaking from the perspective of the "weird" kid - who turned out okay!
One other thought... have you considered music? It's an activity that does not require a lot of social interaction up front. However, there are recitals 1 - 2 times a year and competitions. If he enjoyed music, these recitals would get him out in front of groups of people. Also, it may help him find a group of kids he has something in common with. If he stuck to it, he might even enjoy band or orchestra in Jr. High, which would expand his social network as well.