For the record, if anyone has any idea what causes that message to appear, I'd appreciate it in a post or PM. So before i got the corrupted data message once again, I managed to runs some tests with a high spellpower mage build in Awakening. It goes without saying both the Constitution and Willpower armor runes also carry over, but you'll have better things to use for your armor slots. I have to assume the Dodge runes work while shapeshifted, but it's not really something I can verify. You're pretty limited as far as barrier runes acquisition, but you can increase your shapeshifter's armor with them if interested. There are a couple of other runes that I noticed carried over-Immunity, the anti-fatigue ones, and the Barrier runes.
There might be one rogue in golems(been a while since i did it), so you'll be relying more on your weapons, items and Intensifying runes there and in the Morrigan DLC than you do in Awakening for critical chance/damage.There are no rogues at all in the Morrigan DLC, which was a bit of a disappointment to me there. That's a good thing, because you'll be much more limited in rogues and subsequently Song of Courage post Awakening. One thing I can finally confirm, having recently done the Morrigan DLC again, is that Intensifying runes do carry over while shapeshifted.