It also seems like there wouldn't be much room for fish to swim, at first there would be plenty, but once the corals grow in it seems like it would be cramped for fish activity.
I think getting rid of that big white rock on the left and turn it into a little island (for whatever coral), then get rid of those two white rocks in the center tower island, again have a little island, and then maybe get rid of that tower on the far right... or have a third island. Might be aesthetically pleasing and allow you to see stuff behind it better - just my opinion.
For water protection, there are stains which have a polyurethane within them. You could try using those, a few coats should do the trick.