Getting these runes are not too difficult. Play on Squire Mode and make sure to stock up on 5 potions before hand. You can quit out after you get them. For the Zafira Faris stage - During the second part of the stage, just before the checkpoint you have to strike an eye that is on the top of a wall. Once the eye closes a metalic grate will open ahead on the stage, inside this grate there's the rune.
Here is the link to the complete guide: