I have the same problem, but here the spine bone is set up correctly, so are all the other bones. This MetaRig is made of 2 rigs, a face rig that I did earlier, then I made a new MetaRig which I combined with the face rig correctly. Earlier I was getting the error saying spine.004 was disjoint, but I fixed that by connecting it to spine.003 using the connect button.
Your fix for "Spine.004 is disjoint" was not exactly a fix. It just removed the error message and created further problems. It's not your fault, Rigify setups are just easily messed up with by making small changes.
If you have trouble snapping the bones together, here is how to do it: