Yeah, a video of him on lungeline and with you riding would be great.
How well does he back up? will he back up straight, or in an arc, and if so, curving in which direction? (this applies to how stiff he might be on one side of his body)
I suspect that his issues is not so much pain, like lameness pain, but rather real body stiffness.
I would trot him out more , more vigorously, so that his back is really moving more, and allow him to place his head where he wants for abit.
work on transitions from walk to trot to walk, a LOT. Then, trot to canter, canter a very short amount, then back to trot.
walk him kup and down hills and put out poles for him to walk over. all things to build up his balance and abdominal strength.