The animations still don't work as they didn't before...
Ea is not going to fix your object animations, ever; the tool at TSR will fix those for you.
...but now the custom hair and clothes aren't working.
The clothes are just invisible and the hairs either come up bald or have some kind of base color and that's it.
Any suggestions on what to do to get all these working again?
Invisible CAS CC most likely means you're missing the meshes. Does the CC require any specific EP or SP? Are there any Meshes to download separately?