yeah, if you fill the top of your wood pile with moss, it will eventually form a cloud that let's the bottom act more like caves. I'd also be considering a larger wood. Manzanita and malaysian driftwood shouldn't leech as much as you're complaining about... but a good boil and a month of carbon filtration would help a lot too... thing is, the tannins can be a benefit to your system, it's too bad the color bothers you so much. You might notice it less with more green in the water. But really, I don't see much staining in your photo.
With a tank that large as a mostly empty slate, I would focus on filling in the back corners first, while looking for a nice, tall, branchy centerpiece, that gives some dimension to the upper middle of the tank. I'd also try to terrace the floor up towards the back corners, supporting it with the smaller bits of wood and stone, and planting those areas with plants that appreciate the deeper rooting space, like willow hygro maybe.