Been there, fought that battle. My DS's dysfluencies are not stuttering, so I don't have a huge amount of specific experience. My DS has oral motor apraxia, which means that he cannot sequence the movements in his mouth to say the sounds in the right sequence to say the words he's reading.
The first step is to name the disorder, document it, and share the information with the school. Request a 504 plan for your child, and the 504 plan should read that the child's reading level is evaluated independently for fluency, oral reading fluency, comprehension, and decoding, and that each skills is to be taught at his readiness level.
In practice, it's a nightmare. It does get better as the emphasis tends to move away from oral fluency.
