So I have an idea of what I did wrong, I am just not sure how to fix it.

I used the Unity Glass mod: http://www.omgubuntu.co.uk/2012/07/unity-glass-offers-refined-new-look-for-the-unity-launcher

After removing it, I cannot reset unity and it does not work.

Even after purging Unity and reinstalling it, I cannot seem to replace the missing files.

$unity --reset
WARNING: Unity currently default profile, so switching to metacity while resetting the  values
unity-panel-service: no process found
Checking if settings need to be migrated ...no
Checking if internal files need to be migrated ...no
Backend     : gconf
Integration : true
Profile     : unity
Adding plugins
Initializing core options...done
compiz (core) - Warn: failed to receive ConfigureNotify event on 0x1c00027

Initializing composite options...done
Initializing opengl options...done
Initializing decor options...done
Initializing vpswitch options...done
Initializing snap options...done
Initializing mousepoll options...done
Initializing resize options...done
Initializing place options...done
Initializing move options...done
Initializing wall options...done
Initializing grid options...done
I/O warning : failed to load external entity  "/home/arcline/.compiz/session/10b624e5c8f98c5325134625607758338300000051770001"
Initializing session options...done
Initializing gnomecompat options...done
Initializing animation options...done
Initializing fade options...done
Initializing unitymtgrabhandles options...done
Initializing workarounds options...done
Initializing scale options...done
compiz (expo) - Warn: failed to bind image to texture
Initializing expo options...done
Initializing ezoom options...done

(compiz:7038): Gtk-WARNING **: Theme parsing error: gnome-panel.css:28:11: Not using units is deprecated. Assuming 'px'.

(compiz:7038): GConf-CRITICAL **: gconf_client_add_dir: assertion `gconf_valid_key (dirname, NULL)' failed
Segmentation fault (core dumped)