I reset and rooted my Nexus 5, and then installed Nethunter 3.0. After running Nethunter, I'm unable to add Metapackages. Running apt-get update fails with a bunch of errors:

W: Failed to fetch http://security.kali.org/kali/dists/...armhf/Packages 404 Not Found
W: Failed to fetch http://http.kali.org/kali/dists/sana...armhf/Packages 404 Not Found
E: Some index files failed to download. They have been ignored, or old ones used instead.

I tried modifying the sources.list file, and symptoms changed, and I could actually install a few packages, but others fail, apt-get update fails, and Metapackages fail.

How can I fix updates?