Cycle issues?

[gregzz4]

You haven't mentioned what your PO4 is at, or what levels you had when you were 'cooking' your LR before you introduced it to your system
When you 'cook' LR, you are best to reduce it to zero readings of both N03 and PO4; of course well beyond NH3

If you cooked your LR properly you would have been doing regular weekly water changes to remove the stuff you didn't want in your DT
Having an N03 reading as high as your's leads me to believe you didn't fully cook your rock
Plus, IMHO, having that much rock (180-200lbs) is enough for a 400+Gallon system. You haven't stuffed all that LR into your 90G tank, have you ?

3" of sand is a lot. In my opinion, you're in between a regular 1" bed and a 'deep' sandbed. Do you need that much ? Others will speak up, but I'm thinking it's too much of everything, and it needs some re-thinking ...

I'd suggest you remove a whole lot of that rock, such as reduce it down to maybe 90-125lbs, and then you'll still have to 'cook/cure' it before you can stabilize your N03 readings
Plus you'll actually have room for corals

Get that rock down to zero readings for both N03 and P04, then you can start building a great tank

But this is just my opinion based on what I've read here and what I've done, so take it for what it is ...
Good advice from knowledgeable/opinionated people