This sounds pretty familiar. I have one like that.
First of all, therapy is a must. It is hard to line up, but you sound focused on that.
You are dealing with fragile self-esteem. So it helps if success is a high probability. There are probably other issues in the bundle, primarily OCD. So in order to keep his interest, for sure pick something he's interested in, with a high "cool" factor.
Apart from that, given his age and situation, I would look really hard at the possibility of bullying going on. Mine has a lot of PTSD from versions of that that have caused some problems.
I have really fond memories of doing stuff with my dad like bench carpentry.
Bill