Hi knitting my ds is the same age as yours and in Y9 of a small, independent MS school, which is an out of area LA placement, supported by a statement (about to be transferred to EHCP). He has ASD, severe anxiety and slow processing, plus handwriting issues that means he uses a laptop, although is classed as not having any LD's.
The school he is in was renowned for being excellent at supporting pupils with a similar profile to ds, as well as those with dyslexia and/or ADHD. Unfortunately, the head that put all that support in place left over the summer just before ds started and Y7 was truly diabolical, despite there being a max of 12 per class and an extremely high level Learning Skills Support, plus school SALT.
It took until the Spring term of Y8 and the second SENCO they'd had since he got there, to get them to even begin to implement his statement properly. As soon as they did that, plus allocating a specific LSA to support him organisationally, his grades shot up and have continued to rise this year.
We are now on the third SENCO in three years, but this has been the first Autumn half term that he hasn't had a minimum of a week off with stress/anxiety and he actually seems to be happy at school. Again, this is evidenced by his grades going up and them already wanting to speak to us about moving up a set.
Having gone through two and half years with ds1 there, I am 100% sure there is no way he could possibly have survived in a mainstream secondary. Ds2 is at the local one (that refused to take ds1) and there are 1600 pupils over an enormous site with far fewer LSAs.
Socially, ith as been a huge quandry. He had a small group of lovely friends, but has also been horribly bullied by the 'popular' lads and is despondent about being at the bottom of the popularity heap. We keep an open dialogue about this and try our best to get him to understand that true friends are important over popularity. We had a breakthrough this week when I explained how artificial the school social environments is and about a schoolfriend of mine that was super popular and led the pack, but couldn't hack it when school finished and they realised they weren't top of the heap outside of a school playground.
I have to admit, we have come close to pulling him out and homeschooling so many times and we still aren't 100% sure we've done the right thing by keeping him in school, but he is highly sociable, wants friends and enjoys his friends company and in all honesty, I couldn't offer him that level of social opportunities if he were homeschooled.
I don't envy you the decision. Sometimes I think all we can do is keep moving forward, hope we've done the right thing and act quickly, when an if we sense we've taken a wrong turn.