I think Telemark hit the nail on the head, pretty sure it's burr knots. There is not much to be done except to scrub them off, but I think that might give other diseases an entry point. If you do that, make sure you coat it with some sort of coating (TreeKote). Personally, I'd cut my loses and replace the tree with a healthy new one now, before you have any more time invested. I guess grafting is an option, but the problem may be in the rootstock, and, I think a graft that low will take years to get to the height of a new bare-root tree. Either way, good luck!
https://ipm.missouri.edu/MEG/2015/12/Getting-to-the-Root-of-Burr-Knots-on-Apple-Trees/