My DS was older than yours by the time his PANDAS was such that it really made school an issue, but I can certainly relate to what you're currently experiencing as my DS first got a "regular OCD" diagnosis at the age of 6, just a few months into his first grade year.
Do you have a therapist involved in your DS's overall treatment plan at this point? Obviously, we had one because we couldn't get anyone to sign on to PANDAS at the time, let alone treat it, but he was a good resource for in-school and at-home strategies for addressing our DS's OCD (mostly perfectionism, which led to either