But...d4's have 3 different sides showing at once...if you have 1 rune per side then how will you tell which rune is the one that is showing? Or are you envisioning a traditional d4 that has 3 runes per side?

Well, yeah each d4 "rune" would have 4 results. You could either just have 2 identical results on each die to represent each rune token, or change up the way the runes work a bit so you have 4 different results for each one.

I think I'd prefer some nice gray acrylic tokens with the appropriate colored runes on either side. From what I saw there is a set configuration of the runes. At the moment I rather like the idea of "tossing the bones" to determine how the round plays out. I'm sure that the randomness will irk me at some point in the future but the idea is one that I like.

Or D6's for the runes