You need to inform yourself and learn to fight for him instead of being so passive. If you carry on the way you are, you are going to get walked all over and he will suffer as a result.
The school are exploiting your naivety and passivity. Don't let them. Don't trust them blindly when they've already engaged in unlawful actions (the LA does not have the power to displace the law, I am a little shocked you bought that).
Stop viewing them as being your guide through this and independently inform yourself so that you can assert yourself and advocate for him when he is being failed and you're being fed bullshit. They are not on your side and are not there to help you.
Just because they tell you the unlawful things they're doing are fine doesn't make it true! You need to be able to say "no, this is not acceptable" when this shit is happening.
You need to start fighting for him. Pulling him out of school is the opposite of what needs to happen. It is what they want because then they can wash their hands of him.
Sadly it's been this way for decades and children with additional needs are regularly forced out of the education system if their parents are unable to fight for them and stand firm. Being meek and polite and amenable and accepting does not cut it.
You need to be assertive and determined and unrelenting. You speak up when something wrong is done. You challenge when you are spun a line.
You want him to get the support outlined in his plan? Then fight for it. Don't take the bullshit. Don't watch them treat him in unlawful ways. Don't facilitate their discrimination. Don't thank them for failing him. Don't apologise for his needs and differences.
Demand to know why they keep failing him. Tell them it is unacceptable. Refuse to be intimidated into doing something against his interests because they can't be arsed to educate him appropriately.
You are going to have to keep up this fight for him throughout his education - start as you mean to go on. Stop letting them use you as a doormat.
If this post pisses you off then good - use that to power you to stand up to this unjust treatment by the school.