It seems we have the exact same horse problem. My horse has had a head shaking, bit-grabbing problem for a long time, actually ever since I bought him. About 18 months ago, he was having some odd lameness issues where he was slightly off and vaguely not right. It took my vets months before testing for EPM. He was positive, so I started treatment with Protazil and ulcer meds. (EPM can cause ulcers.)
He improved, but was still not right. This summer, the connection problems got worse, so I had major work-up done. His head, back, TMJ, and stifles were x-rayed. The X-rays revealed remodeling in his stifles. Why, I have no idea. He has never been in “hard” work. He was injected with a steroid and polyglycan. The improvement was dramatic. The fussiness with the contact is almost gone.
His EPM titer levels have dropped dramatically, from 2560 to 320. I’ll keep him on a 1/2 dose daily of Protazil until the number drops below 40.
If your horse was diagnosed with EPM, there is likely nerve damage that makes it hard for him to use his muscles properly. I think you are on the right track to do ground work. It takes a long time to regenerate nerves.