Thanks for the suggestions, all the bone objects were originally grouped together and exported, so the UV mapping might be an issue, but even after combining all the bones in one mesh with one UV map, copying all the weights over, deleting history, removing influences, limiting influences and so on, none of these had any effect on the upload model except for reducing upload cost and complexity because of the combined mesh. So while I'm certain the UV map has only one set now, textures still don't map correctly when uploaded to SL. The only nodes in the attribute editor for each LOD of the model only has the mesh and materials so I'm certain there's nothing left in the history.
I mapped the influences so that only one joint applies to each skeleton bone object, as there's no need for mesh deformation when animating a skeleton. I'm not sure if this would cause any issues or not. I haven't deleted any bones, and I tried mapping the spine and ribs to different joints to no effect on the 'missing' joint. I have seen some custom avatars that have a skeleton object worn with the avatar, but I don't understand why I would need that since the base skeleton hasn't been significantly altered other than moving joint positions to match the exact points of rotation. I don't know how you would upload just rigging anyways.
So again I guess I'll just try it with Blender later. Maya is ridiculously unstable for a 'industry standard' program, crashing over the slightest things.
I can run Cmake, but attempting to compile the OpenCollada master just gives me the error, "configuration error, your project files may be invalid", no matter what version I configure VS in cmake, even though the cmake files are clearly in the folder.