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First let me say that the look of the tank is generally good.  The coral appear healthy. There is good coralline algae growth. A Nitrate level of 20ppm is not bad. I don't think you need to worry. Each tank finds it's equalibrium over time, but just for the heck of it, I'll give you my opinion on a few things you could do to tweak it to a higher level of health.
It looks like you must have traded crushed coral substrate for CaribSea Special Grade Reef Sand, correct?
How deep is the deepest area of sand and how shallow is the shallowest spot?
Do you know that a small amount of Oolitic sand has solved the Nitrate problem for many tanks? I'd carefully place about a quart of Oolitic underneath the existing sand on each side as close to the back as possible. (That's two quarts) You were right about the guy from The Aquarium not giving you enough sand.
What's the GPH of the return pump?
It appears that circulation is two maxijets (size?) with fan attachments and the sump/Refugium return. Those fan nozzles on the return are dispersing the power of the return water. I would remove all the fans. GPH means nothing if the circulation is not powerful.
Do you know how to turn the maxijet nozzles to point upward without the need for the fan attachments?
I would place one maxijet diagonally across the surface so that it intersects the flow from one of the return nozzles (depending on the GPH of the return, I might even take off the "Y" so there is just one nozzle.)
What size/wattage are the PC tubes in that light fixture over the refugium? It looks like 13 or 18 W. It's hard to find a manufactured Refugium light that beats the DIY alternatives. They grow Macroalgae like crazy.
Could you find a way to increase the Refugium substrate surface area?
There isn't enough Macroalgae in the Refugium in this pic and there is LR rubble covering the sand. Remove the rubble. Sand cannot do it's job when it is covered with rock.
I would swap the LR compartment for more substrate and algae. Sand has many times more filtration capacity than LR.
What's the purpose for that little powerhead in with the return pump? If it's to keep a pile of detritus off the bottom, I'd remove the PH and allow the detritus to settle and then remove the little pile periodically.
The placement of the skimmer before the Refugium is making the skimmer pull out more than it needs to. Having the skimmer after the Refugium allows the refugium to benefit from all the nutrients that come down the drain. But I'm not sure anything can be done about this, so forget I said anything. 
Please describe or show a good pic of the aquascaping from an upward angle. What kind of structure and how open is it, especially over the sand? Placement of a powerhead (the remaining one) in the back behind the rock, pointing down, to create circulation through the corner did wonders for filtration of SMatney's 90 gal corner tank. Circulation over the sand increases filtration capacity.
You said the old LR was in pretty bad shape. Where did the new LR come from and what did it look like?
Do you know what it means to submerge, turn, twist and shake the LR when moving it from store to tank or from tank to tank?
That's all for now. Looking forward to further discussion. 
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