I'm not a teacher, but I'd say if the boy is enjoying what he's learning and practising then there's no harm in letting him keep working for the grade 3....
Or maybe if he's not too attacted to the idea of doing the grade 3 right now, then maybe take a bit of time out of exam practise to work on the things that he's not so confident on - like working on some simpler songs to help him become more confident in co-ordinating both hands.
As you say he learns mostly by ear, perhaps you could try out improvising around a certain theme (which may be written down) that he is having particular trouble with. If he hears you playing it right, and can see the notes at the same time, perhaps he might begin to develop a link between what he hears and what he can see written, and then try it out for himself.
But as I say, I'm not a teacher nor do I know about dyspraxia and so I may just be talking a load of rubbish!!
Good luck

Laura