I am a former teacher, and I've taught 4 kids (ages 7-12) with Asperger's. That social skills group is a great start! If possible, take your son to counseling outside of school as well. Find a fantastic counselor or social worker with experience on the autism spectrum. He or she can really work, in depth, on those social skills, as well as the emotional side. A common issue for children with Aspergers is difficulty understanding their own emotional reactions to social situations. Frequently puberty can be very hard for them, because their emotions become so much stronger and can feel out of control. (Where before, they may have had limited emotional responses.)
Talking, one on one, is crucial! A counselor can really help your son understand his feelings, and learn how to react appropriately in social situations. It will build nicely on his after school class.
Also, you keep talking to him! (Which I know you already do!) Ask him questions all the time- and make them "why, what, and how" questions, so he won't just give you yes or no answers. Ex: What was the most fun thing you did in school today? How hard was that math test??? Why did you seem so frustrated when you got home?
While your son may not be big on looking you in the eye, he can still be reminded to stay on topic. Help him learn to answer your questions fully, with real opinions of his own! Ask more questions to follow up on his answers, and show him how interesting you think he is. :) You can role play solutions to social problems, too. Make it fun- using games, music, or examples from TV.
Finally, keep an eye on him at school. Bullying can be a huge problem, and sometimes isn't dealt with appropriately by teachers or staff. Your son may feel awkward socially, and may not know what to do when kids are mean to him. Middle school is a rough place to be different. So talk to his teachers, check up on him a lot, and again- ask him a ton of questions!
All my students who were diagnosed with Aspergers have gone on to be very successful in school- it usually accompanies intellectual strengths in different areas! Find what he loves to do, and he'll thrive. One of my old students is in college this year...makes me feel so proud (and old)! The others are in middle school and high school, and doing great!
Enjoy your son!