Ok, so I did a bit of a rescape. As per shrimpnmoss's advice, I took out half the wood (I chose the piece that didn't have fissidens already growing on it). I also added more squares of moss, more java fern, and red root floaters (thanks, Green_Flash!).
The nitrites are down below .25, but the test is still turning a slightly darker blue than then pure color when you start, so the tank isn't
quite ready yet ...