Well, it's obvious that you are improving his body, so you must be doing something right. So, he no longer rides in the martingale?
I think there are lots of threads on how to get a horse to build topline, or to ride "long and low". All of those things can help build up the upper neck muscles and relax the under muscles. Any kind of riding that does not have the horse coming above the bit and bracing against it will start to relax the lower portion, and to build the upper, you encourage the horse to lift it's neck up from the lower portion (where it comes out from between the shoulders) and arch the upper portion, and break AT the poll, not part way down the nect.
Read what you can by Dr. Deb Bennet. She writes about the anatomy of horses and tons of stuff about conformation and how to develop the neck muscles. Her articles are in Equus magazing. Look at their back issues and read her articles in sequence. You will learn a lot.
By the way, I jsut had to say how much it irritates me when people say, "he's a pretty nice horse, for an Appy". He's a nice horse , period.