The previous owner of my bike had plastic patches everywhere the cables rubbed. Yes, there were a lot of patches all over the place.
I dealt with the rubbing at the head tube by running:
Rear brake line on the intended brake line guides on the non-drive side of the top tube.
Rear derailleur cable entering the front middle cable stop and exiting the rear drive side cable stop.
Front derailleur cable entering the drive side cable stop and exiting the rear middle cable stop.
I'm using that old trick of crisscrossing the cables in order to get better routing for the housing. This routing that I'm using keeps the cables completely away from the headtube.
The only rubbing left to deal with now is the rear brake housing rubbing on the seat tube. I guess the patches have to go somewhere.