Roger - I've done this with people with neurological damage from a variety of causes. You're on the right track; one suggestion - take a big step back and look for those tedious excercises that we used to train our responses when we were first learning. Many of them were written by some pretty smart teachers, and they really work because they take out the need to make a good job of a tune you already know and get on with the business of building, or rebuilding the specialised pathways all musicians need. Look among the classical guitar tutors (which is where I come from) and the violin studies (which is where I definitely don't...).
Good luck - pm me if it you think I can help.
KYBTTS