By massive cleanup, do you mean you sold a lot of cards? That's probably a bad idea, since you could have used them in a better upped deck.
As for the AI3 deck, I don't think it's worth upgrading, but you could try to find a better unnupped one. Since it has a 90% winrate, upping it won't change that much. Also, the rewards for AI3 are fairly small, so you should upgrade decks with a more profitable use.
Now, for the other two, it depends on how upping it would affect it. If one's winrate increases significally when it's upped, up that.
This is just my opinion, so you should listen to others before deciding which to upgrade.