Hey, sorry to hear it's not quite working for you. The Redshift.txt is a settings file for Classic Theme Restorer. It moves Firefox elements, not the lines on the theme. To fix this, I suggest installing the Classic Toolbar Buttons add on, and play around with the "Extra top & bottom space for..." settings until it matches up with the theme.

UPDATE:
I've updated the layout instructions. Please try following the updated tutorial to see if it helps with your alignment issues.