Thanks everybody for the helpful replies.
I'd better check our settings on Word - it seems to find spelling and verb agreement problems, but I'm not sure about run on sentences. Unfortunately, he still has to hand write most assignments at school, so this would only help with projects at home.
I like the idea of working on clause analysis with him. He is Mr. Logic, so this might help. He has done quite a lot of work on finding the subject/verb/direct object/indirect object, etc at school, but I don't think they related much to punctuation. He goes to a French school and the grammar is pretty rigorous (compared to what I remember of English school in the 1970s).
Last summer, he had a creative writing project that he was very motivated to do - I used the project to work on choosing the right place for periods, mostly by reading it aloud with him. I'm not sure it helped much. He is probably a bit weak on auditory, so maybe this wasn't the best approach. He also has always hated reading aloud, although has been a voracious silent reader from an early age.
When he first started to write, he didn't leave any spaces between words. He would write a page long story without a single space! Somehow this seems related . . .
