You are his mother, and know whether or not he is well enough to go to school and how much is too much.
But I am going to have to take the side of the school a little bit. I do not think that the truancy officer contacting u was that major of an issue. As u said once you explained, it was cleared up. They were just following their policy, which I know u said u were unaware of, but I bet if you look at the school handbook, they give u at the begining of there year, it will probably list this policy.
We have never bothered with an IEP or 504 and my child is in 4th grade. Just never needed it, our school is very good, and I know I can get one if it would be needed, but don't anticipate needing one. Really does it get u anything? I can't think of anything it would get, because the school is already voluntarily accomidating.
You say your child is struggling, and u believe it is a confidence issue....not sure what help u could get with this in an IEP or 504, but prehaps you could speak with the school counselor or the social worker at your clinic. Did u requested the work he missed when he did not go to school?