How do remove "Ignoring file in directory /etc/apt/sources.list.d/ as it has an invalid filename extension?

To fix your first problem run this in a terminal:

sudo rm /etc/apt/sources.list.d/*.disable

(An older version of the package management tool left these files when you disabled the PPAs. Removing them is pretty safe)

Your second problem comes from and old Karmic repository. To find out which one run this in a terminal:

cd /etc/apt

grep -rw karmic *

Once you know which repository it comes from it would be easy to disable/remove it.

maybe you should try this command:

sudo sh -c "echo 'Dir::Ignore-Files-Silently:: \"(.save|.distupgrade)$\";' > /etc/apt/apt.conf.d/99ignoresave"