Hey, thanks for keeping it up.
Sorry to hear you injured yourself :/ Hope you get well soon
With regards to the mesh, I'm not exactly sure what happens, but I'd try to avoid bones named like so <bone name="DEF-Bovidae_ReartLegTop_L.001"> especially when a bone is named <bone name="DEF-Bovidae_ReartLegTop_L">
I'll try to look in more details tomorrow.
Also when opening your blend file it says it's missing a python file for the rigging ui, any addons I should have ?