Hi mouseling, oh it's dreadful the damage an inexperienced teacher can do, she clearly has no understanding of boys. I do have to admit though, before I had boys of my own I misunderstood some boys' behaviour as naughty, and looking back it wasn't at all.
It seems to me that you are doing all the right things to support your ds though, and with his regular teacher back and a meeting with the SENCo things are moving in a more positive direction. I think if you explain to them both that you have a happy and bright little boy at home, and that you are worried about his motivation at school, they should be understanding. It is just a shame you do not seem to have a very supportive HT, maybe he/she was feeling defensive when you spoke to them last?
It has really helped me to have daily chats with my ds' teacher, and it is interesting that whenever my ds has a supply teacher (she is retired and v v experienced) she has nothing but good thingsto say about him.
I have discovered many people with ds who have also been through a really difficult time at school at about the same age, and I think it has a lot to do with boys' social emotional and behavioural development being slower than some girls', but also inexperienced teaching. Which is why the boys are better at home.
Good luck with it all, I will try to catch up with you soon.
x