Errors and many configured multiple times in sudo apt-get update for Ubuntu 16.04

This is what I get from sudo apt-get update.

michael@16:~$ sudo apt-get update
[sudo] password for michael:
Hit:1 http://ppa.launchpad.net/nilarimogard/webupd8/ubuntu xenial InRelease
Hit:2 http://ppa.launchpad.net/nowrep/qupzilla/ubuntu xenial InRelease
Hit:3 https://deb.opera.com/opera-stable stable InRelease
Hit:4 http://us.archive.ubuntu.com/ubuntu xenial InRelease
Get:5 http://us.archive.ubuntu.com/ubuntu xenial-updates InRelease [102 kB]
Get:6 http://us.archive.ubuntu.com/ubuntu xenial-updates/main amd64 DEP-11 Metadata [303 kB]
Get:7 http://us.archive.ubuntu.com/ubuntu xenial-updates/main DEP-11 64x64 Icons [184 kB]
Get:8 http://us.archive.ubuntu.com/ubuntu xenial-updates/universe amd64 DEP-11 Metadata [121 kB]
Get:9 http://us.archive.ubuntu.com/ubuntu xenial-updates/universe DEP-11 64x64 Icons [145 kB]
Get:10 http://us.archive.ubuntu.com/ubuntu xenial-updates/multiverse amd64 DEP-11 Metadata [2,520 B]
Hit:11 http://archive.canonical.com/ubuntu xenial InRelease
Get:12 http://security.ubuntu.com/ubuntu xenial-security InRelease [102 kB]
Get:13 http://security.ubuntu.com/ubuntu xenial-security/main amd64 DEP-11 Metadata [68.1 kB]
Get:14 http://security.ubuntu.com/ubuntu xenial-security/main DEP-11 64x64 Icons [43.0 kB]
Get:15 http://security.ubuntu.com/ubuntu xenial-security/universe amd64 DEP-11 Metadata [19.4 kB]
Get:16 http://security.ubuntu.com/ubuntu xenial-security/universe DEP-11 64x64 Icons [25.6 kB]
Get:17 http://security.ubuntu.com/ubuntu xenial-security/multiverse amd64 DEP-11 Metadata [212 B]
Fetched 1,115 kB in 12min 1s (1,545 B/s)
AppStream cache update completed, but some metadata was ignored due to errors.
Reading package lists... Done
N: Ignoring file '20auto-upgrades.ucf-dist' in directory '/etc/apt/apt.conf.d/' as it has an invalid filename extension
W: Target Packages (partner/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Packages (partner/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Packages (partner/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Translations (partner/i18n/Translation-en_US) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Translations (partner/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target DEP-11 (partner/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target DEP-11-icons (partner/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Packages (partner/binary-amd64/Packages) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Packages (partner/binary-i386/Packages) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Packages (partner/binary-all/Packages) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Translations (partner/i18n/Translation-en_US) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target Translations (partner/i18n/Translation-en) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target DEP-11 (partner/dep11/Components-amd64.yml) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
W: Target DEP-11-icons (partner/dep11/icons-64x64.tar) is configured multiple times in /etc/apt/sources.list:43 and /etc/apt/sources.list.d/xenial-partner.list:4
michael@16:~$

I expect to have more numbered lines than 17.
Been trying to remove the line N: Ignoring file '20auto-upgrades.ucf-dist' in directory '/etc/apt/apt.conf.d/' as it has an invalid filename extension
I read that, must unmount before removing. Unmounted and started to remove. Stopped at when warning statement, you may damage this because file is mounted. Could not figure out how to remove the configured multiple times.
Getting older, and have noticed that, I sometimes can't see the forest for the trees. Any help appreciated. Also another problem, very slow about certain actions, as in above line. Fetched 1,115 kB in 12min 1s (1,545 B/s) Don't know if related. I am working on it as different problem.