Hi WVUReefer!
So lots to deal with here! Lets begin with your typical regimen and filtration. One important detail I'd like to ask about is the timing of everything. This problem your reef is suffering takes a while to solve.. and I want to ask about what solutions you've tried and more specifically how long you've tried each for.
In a vague description (Until we get more information) here's what I would try for your situation:
- I just don't recommend dosing anything (Especially carbon dosing) as it is royally complicated to get right and requires quite a bit of time tweaking. Unless you have been doing it for a while.. I would just halt it for now.
- With the visible problems (Algae/cyano/etc) I would export them as soon as possible via manual removal. It isn't fun but it's the best way to remove the problem and the cause of the problem (Phosphates, "funk") at this stage of the game.
- What's your waterchange schedule? I would try a pretty typical regimen of about 10% per week for now. Doing none is not recommended, and too much could actually cause another problem via livestock stress, etc.
- This one is pure theory on my part and take it with a grain of salt: I am not a fan of refugiums as filtration, but I believe them great for other things. I would not depend on this method to truly help your problem out. Adding more plants won't help you out.. again just my meager opinion.
- You probably already do this, but run your skimmer wet, better to grab as much as possible and correct salinity than possibly not grab the extra funk from the tank.
HTH for now. Keep us updated.
Christian
