OTGMom, our DSs also attend parochial school. I got the "we're very good at teaching the kids in the middle -- if your DS needs special attention, we don't have the resources so maybe you should go elsewhere...." answer in K and 1st. This year, I made some small headway by dealing directly with the resource teachers. It is a very difficult situation if your principal is not open to change as they don't HAVE TO accommodate you. I've worried that if we did apply to DYS, got accepted, and received advocate assistance, we'd just be in a pickle, because the school could very easily say that we should leave because they can't provide accommodations. I think it's a tight line to walk.
Best of luck with it!