Yes, Yes and Yes... I would let more roots come out the side of the rooting cube but please make sure that the roots do not see direct light or they will stop growing that is why it is important to have it in a rooting tray or something dark so the roots never see the light. I always put some hydroton (clay pellets) in the bottom of my soil to allow for the nutrient solution to flush out the bottom and also not to let the soil wash out during watering. I think that the soil you are using sounds fine. DO NOT fertilize this small seedling as of yet because the soil that you are using with the worm castings will support the first few weeks of growth with the levels of nitrogen. Fertilize after 3-4 weeks of growth or when you can tellit has entered the vegetative stage with vigurous growth.