We have a similar situation, but instead of a magnet program, a gifted program starts mid-3rd grade (DD survived screening and is going through the selection process now...it is a LLLOOONNNG process). Since I knew this was coming up, I figured I just needed to be patient, enrich at home (and outside of school at a local gifted center), and look for differentiation wherever possible. The "all leveling out at 3rd grade" myth has not proven to be at all true for us - in fact DD is showing a pattern of staying ahead, while also making rather large learning leaps. This has worked for us, but then again, my kiddos are on the young side of their grades.
It sounds like your magnet program will eventually provide more needed challenge, so I would focus on blazing a path to get him there. Positive, supportive mentors are HUGE along the way (DD was so lucky to get a teacher that really understood her in 1st grade and was so enthusiastic about having a student excited to learn!). It sounds like your son has a special teacher, who will support, challenge, encourage and nurture - such teachers can ignite a passion for learning that blazes for a LONG time!
