I'm thinking his experiments on the bodies and the failure made his psycho.
The fish tanks maybe be The Governors version of Hershel's zombie barn.
Andrea is attracted to power, as much as she's her own person and speaks her mind I think she likes someone who's more powerful than her, maybe to dominate her. But this is MHO.
Without a doubt It has to be the prisoner that Rick left for dead in the yard that is screwing w/them. I don't know how he could have survived, it's either that or maybe.....maybe, the virus is mutating and the zombies are becoming more "intelligent" ????