Thanks for your input, everyone! I don't have a place in the ground for this plant. I was using it to graft onto. The idea was that for every graft on my main tree, I'd do one of the same on this little potted tree. That way, if a graft on my main tree didn't work, I could take a graft from this little tree and try it again. It'd keep me from having to get scions through the mail again. That plan didn't really work out. Too often I'd do a bad job on *both* trees!
I didn't have mulch up close to the bark, so crown rot doesn't seem right. And the disease was spreading in patches that were totally separate from one another -- trunk and branches. So I ended up tossing the plant. No big loss; I'll start another seedling before long, and my in-ground tree isn't showing any signs of this disease.
I think the group consensus is right: some kind of fungal attack that decimates the bark right down to the core. If it happens again, I'll be forewarned and I'll treat for fungus right away.