Hello Yoboyjdizz,
Is great to see that you are setting up your tank. I think some time ago, I saw a thread in which it seamed like you were going to have to sell it even before you even had a chance to get it wet and that is always sad to hear/see.
Any ways, here you are with this beautiful tank and looking better by the day. I really like the islands, the caves and the platforms. If the pocket allows, a little more rock could be of use. Never mind, I see that another 45#s are on the way.
In terms of your chemistry, I would think that your tank is simply going trough its cycle. Maybe a little bacteria addition, macroalgae in your refugium or a water change may help in inproving your chemistry. Another thing that comes to mind would be seeding your tank with a little bit of live sand from other fellow reefer's tanks. You can always trade sand cups with them (they give you a cup of their live sand and you give them a cup of your new/clean sand). You are more than welcome to get some from me, but I am not sure the 3-4 hour round trip drive would be worth it for some sand, but if you are in SF any time, just give me a call or PM and I'll give you some.
Scratches on acrylic are just part of life, but you are very fortunate to have Mr. MarcDaniels just around the corner, in your area. Ask around and you will find that every one who he has worked with in removing scratches from their tanks, have been very happy with his work.
You are sorrounded by great people that are incredibly knowledgeable, so continue your humbleness (keep asking questions) and listen to what they tell you. They will save you lots of head aches.
I wish you smooth sailing with your set up and keep the good work up and of course, the pictures comming.
Again, I am very happy to see you are setting up your tank!