I am starting to think that the only rule based way to apply Awaken to an Animal Companion is to consider base HD of the AC to be the HD of the Animal Companion before being Awakened?
Also, here is part of the language of the Awakened Spell:
"You awaken a tree or animal to human-like sentience. To succeed, you must make a Will save (DC 10 + the animal's current HD, or the HD the tree will have once awakened). The awakened animal or tree is friendly toward you. You have no special empathy or connection with a creature you awaken, although it serves you in specific tasks or endeavors if you communicate your desires to it. If you cast awaken again, any previously awakened creatures remain friendly to you, but they no longer undertake tasks for you unless it is in their best interests."
The success of the spell would be based on the AC's HD at the time it is your animal companion. Does that also lead one to the conclusion that the HD you look to after the spell success would also be the HD at the time it was an AC?
As a practical matter, I don't see how else you could do it anyway.
