I'm not sure what the Vajra are. My original thought was they were some sort defense system left behind by the Protoculture, but now I am uncertain.
I'll quote myself on the Galaxy:
The Galaxy has its own agenda. Brera and the -27's are a part of it, I am sure. I am not sure that Grace is part of it, however. Lots of intrigue here, I would say that not everyone is on the side we may think they are. And then we have Dick Vilrer, not even sure where he fits in yet.
Keep in mind the classic Macross formulas. Alto will have to choose between Sheryl and Ranka, and the Frontier will join forces with either the Galaxy or the Vajra to defeat their common foe.