If there is no light or macro in the sump I would not call it a refugium, perhaps a cryptic style sump without the beneficial organisms, unless they were seeded or have had a long time to establish.
Chaetomorpha is far different then the caulphera's. Chaeto is very stable, needs very little light. It grows mat like, can trap detritus as well as being a safe haven for pods.
There are many species of caulphera. Many are fast growers. they are more volatile then chaeto, but IME do not grow as fast or export as many nutrients.
If the "refugium" is not lit it will not help stabalize pH. Light source for a 20g refugium is cheap. Just get a clip on lamp from HD and a CF bulb. One of the spiraly ones, will cost you less then $20.
As for pH buffer, I think I paid $13 for my bottle.
It is important to either add sand to your display or remove it. 3" will be a continous source of problems. Unless you have a biological means of filtering and stirrig the sandbed, I suggest removing some, JMO. Having a 3" sandbed is not going to work for you, I'm sorry.
Nitrate reactors and plenums are completely different things. To install a plenum at this point you would have to complete tear apart your system. take eveything out, and then install the plenum. While plenum's work great for some people, I don't like the idea of having to tear down my tank every few years to fix it. IMO, IME it is quite possible to setup a long term stable tank using other methods. JMO. I have read Goeman's book, there is also a new article in one of the fish Mag's about Plenum's, which one escapes me, I think it was Marine Fish and Reefs. Had a comparison from the Wakiki aquarium.
A nitrate reactor would be far easier for you to install. The directions on a DIY verision are listed above. They also sell them in a plug and play variety, which after buying one, is what inspired me to return it and make my own.
Hate to break it you ya bud, but with nitrates at 160, a skimmer is not the only anwser.
Your refernce to stuff building up on your rocks and corals brings up another question in my mind. What is the flow like in your system? Are you keeping anything that is flow sensetive. In my reef tanks there is no way anything in the water column could settle on to anything, there is a bunch of flow. In my seahorse tanks which are lower fow the flow is designed to come through the rock work to also minimie the bility for anything to settle on the rocks or corals. JME