I don't know much about Autism services in the Columbia district, but you might check out their website:
http://www.columbia.k12.mo.us.
As far as middle schools go, you should look into Smithton - the kids in our neighborhood go there and the parents are extremely happy with it. I think Gentry would be okay as well, but steer clear of Lange Middle/Oakland Junior High. My husband is a teacher at Oakland and was (not so pleasantly) surprised by the apathy of the students there. The principal and teacher quality is excellent, but they can only do so much when such a large proportion of the students (and parents) don't seem to care if their children succeed.
My husband loves teaching in the district - Columbia is truly committed to paying their teachers well and he's had nothing but good things to say about his principal and the administrators in general. Get your application in early - apparently last year they got over 1200 applications for about 200 positions!
Welcome to Columbia!