Updated Ubuntu 16.04, now I'm running Kali?

Yes, you are now using Kali.

I consider this far too destructive and I would file a bug report for this if I was you. Our upgrade should not upgrade you to another (aka. unsupported by Canonical) operating system. Either it should give a big fat warning that there is a personal archive or it should automatically disable manually added personal archives.

What happened is that all packages got updated and those related to Kali also pulled in anything related to Kali. Making it cascade into replacing your system with Kali.

You can remove Kali by disabling their archive and then execute ...

sudo apt install ubuntu-desktop

but ... it will likely be easier and quicker to re-install if that is possible.

OP Update:

I was unable to get the Kali archives removed and migrate my install back to Ubuntu 16.04. I decided to cut my losses and install fresh, but didn't want to lose any data.

Backup

I booted to the Kali console and logged in to my old user account. I then Used sudo fdisk -l | more to get a list of drives after I plugged in my usb drive. The new drive was /dev/sdb1.

Tip: I made sure that I had enough space on my drive by using du -sh * while in my home directory.

To mount the drive, I issued the following:

sudo mkdir /media/usb/
sudo mount /dev/sdb1 /media/usb

I then copied my files using cp -rv * /media/usb/.