I wish I had an answer, but unfortunately I have a similar problem. I feel like in my case, though the latch looks great, there must be a latch issue on the right side because after nursing, the nipple often looks pinched. Does your nipple ever looked pinched? Also, perhaps of note is that my right side is larger than the left, so perhaps that plays a role.
He nurses great on the other side - we've been totally pain free for months. I was off lanolin for a long time because we had thrush, but have been using the lanolin more lately and that seems to be helping. And I am working to ensure a perfect latch when I can (making sure there's flange on both sides of the mouth on top and bottom), but we like lying down nursing, and once he starts to get sleepy, it's hard to keep his latch intact. Also, while side lying nursing it's hard to see the under side of his mouth to do corrections.
I don't know if it's possibly a latch issue in your case as well, but one thing I've wondered is whether in the case of a one sided bad latch, a chiropractor or cranial sacral therapist might be able to help. Does anyone have experience with that?