I have been going through something very similar with one of my horses. My horses are all barefoot. I ended up calling in a specialist and it turned out that it is the trim on his feet. His heels are too short, his toes too long and his soles are thin. He had some bruising, I would never have been able to see them but they were there. So his trimming protocol is changing and the specialist will be doing his feet until we get things right for him. There is an old saying "no hoof, no horse.
I am not saying this is the problem but my horse would move like he was stiff and he was sore from compensating. He has had several chiropractor appointments as well as is definitely doing much better.
I just wanted to share my experience with you because I know how frustrating it is trying to find the root cause so it is just something to keep in mind.