A year ago my nitrates were over 200 and after adding a nitrate destroyer reactor I've been able to get it down to 30 or so (I need to test to make sure it's not much lower!). Actually 40ppm isn't a bad value at all. I have the opposite problem with phosphates so I continue to use GFO to reduce them (also need to test again!).
I have typically had the same issue not being able to keep millepora... although I currently have 2 and they have been doing really well for a couple of months. Staying colorful and fuzzy! I really don't know why though. But I'm at the point where I will just keep whatever is doing well and not sweat the rest of it. I like the look of a smaller number of big colonies so whatever corals give me that reef will stay in my tank.