Xenial repositories changed to Bionic after failed upgrade (system nearly broken)

Question

I ran do-release-upgrade and before it started downloading pressed Ctrl+C. When I ran the command again it mentioned:

Please install all available updates for your release before upgrading.

I obliged (apt-get update, apt-get upgrade) but shortly after realized it was updating to Bionic. Here is the partial output of

grep ^ /etc/apt/sources.list /etc/apt/sources.list.d/*

> /etc/apt/sources.list:# deb cdrom:[Xubuntu 14.04 LTS _Trusty Tahr_ -
> Release amd64 (20140416.2)]/ trusty main multiverse restricted
> universe /etc/apt/sources.list: /etc/apt/sources.list:# See
> http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
> /etc/apt/sources.list:# newer versions of the distribution.
> /etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ bionic
> main restricted /etc/apt/sources.list:deb-src
> http://us.archive.ubuntu.com/ubuntu/ bionic main restricted
> /etc/apt/sources.list: /etc/apt/sources.list:## Major bug fix updates
> produced after the final release of the /etc/apt/sources.list:##
> distribution. /etc/apt/sources.list:deb
> http://us.archive.ubuntu.com/ubuntu/ bionic-updates main restricted
> /etc/apt/sources.list:deb-src http://us.archive.ubuntu.com/ubuntu/
> bionic-updates main restricted /etc/apt/sources.list:
> /etc/apt/sources.list:## N.B. software from this repository is
> ENTIRELY UNSUPPORTED by the Ubuntu /etc/apt/sources.list:## team.
> Also, please note that software in universe WILL NOT receive any
> /etc/apt/sources.list:## review or updates from the Ubuntu security
> team. /etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/
> bionic universe /etc/apt/sources.list:deb-src
> http://us.archive.ubuntu.com/ubuntu/ bionic universe
> /etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/
> bionic-updates universe /etc/apt/sources.list:deb-src
> http://us.archive.ubuntu.com/ubuntu/ bionic-updates universe
> /etc/apt/sources.list: /etc/apt/sources.list:## N.B. software from
> this repository is ENTIRELY UNSUPPORTED by the Ubuntu 
> /etc/apt/sources.list:## team, and may not be under a free licence.
> Please satisfy yourself as to  /etc/apt/sources.list:## your rights to
> use the software. Also, please note that software in 
> /etc/apt/sources.list:## multiverse WILL NOT receive any review or
> updates from the Ubuntu /etc/apt/sources.list:## security team.
> /etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/ bionic
> multiverse /etc/apt/sources.list:deb-src
> http://us.archive.ubuntu.com/ubuntu/ bionic multiverse
> /etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/
> bionic-updates multiverse /etc/apt/sources.list:deb-src
> http://us.archive.ubuntu.com/ubuntu/ bionic-updates multiverse
> /etc/apt/sources.list: /etc/apt/sources.list:## N.B. software from
> this repository may not have been tested as /etc/apt/sources.list:##
> extensively as that contained in the main release, although it
> includes /etc/apt/sources.list:## newer versions of some applications
> which may provide useful features. /etc/apt/sources.list:## Also,
> please note that software in backports WILL NOT receive any review
> /etc/apt/sources.list:## or updates from the Ubuntu security team.
> /etc/apt/sources.list:deb http://us.archive.ubuntu.com/ubuntu/
> bionic-backports main restricted universe multiverse
> /etc/apt/sources.list:deb-src http://us.archive.ubuntu.com/ubuntu/
> bionic-backports main restricted universe multiverse
> /etc/apt/sources.list: /etc/apt/sources.list:deb
> http://security.ubuntu.com/ubuntu bionic-security main restricted
> /etc/apt/sources.list:deb-src http://security.ubuntu.com/ubuntu
> bionic-security main restricted /etc/apt/sources.list:deb
> http://security.ubuntu.com/ubuntu bionic-security universe
> /etc/apt/sources.list:deb-src http://security.ubuntu.com/ubuntu
> bionic-security universe /etc/apt/sources.list:deb
> http://security.ubuntu.com/ubuntu bionic-security multiverse
> /etc/apt/sources.list:deb-src http://security.ubuntu.com/ubuntu
> bionic-security multiverse /etc/apt/sources.list:

Some packages of the new release are installed now. If I run

sudo apt update && sudo apt upgrade -f

I get

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 python-rna : Depends: libgsl2 but it is not installable
E: Broken packages

Help needed!