sounds like you are on the right track for sure. keep in mind that trot work can help far more than canter, and also vary headset. to stretch i'll work a horse on a very long rein and allow them to stretch as low as they like at the trot and i find that helps. i'll also do a lot of what you had said - shoulder ins, leg yeilds, transitions, and circles with lots of changes of direction.
good luck and keep us posted on progress! i'm doing some similar work with my horse as he managed to (somehow) strain his neck on the left side mid-neck... and nothing else LOL