I really don't know if the Wooden Dowels will have any effect... no clue. Maybe someone can chime in for that question.
I am a bit confused about matching ammonia levels. You need to have 0 ammonia. I understand some NO3 (nitrate) 0 to 10 is not unusual... as a matter of fact I have never been able to reach 0 and my livestock is doing great. But ammonia will kill all your fish if not kept at zero.
This is a great article about ammonia:
article
Some quotes from the article:
Ammonia is very toxic to marine fish. The mechanisms of toxicity are complicated and are an active area of continued investigation by researchers. Its effects include damage to the gills, resulting in poor gas exchange, ion regulation and blood pH regulation.14 Other effects include hampering oxygen delivery to tissues, disrupting metabolism and toxicity to the nervous system that causes hyperactivity, convulsions and death.14 Ammonia can also be very toxic to many other organisms found in reef aquaria.
also
Because ammonia's toxic effects appear at levels significantly below those that are acutely lethal (0.09 to 3.35 ppm NH3-N or 1.3 to 50 ppm total NH4-N at pH 8.2), and because some organisms in a reef aquarium may be more sensitive than the few organisms that have been carefully studied, it is prudent to err on the side of caution when deciding what concentrations of ammonia to allow in a reef aquarium or related system.
My suggestion is to take some sort of corrective action if the total ammonia rises above 0.1 ppm. This suggestion is also made by Stephen Spotte in his authoritative text, Captive Seawater Fishes.6 Values in excess of 0.25 ppm total ammonia may require immediate treatment, preferably involving removal of all delicate (ammonia sensitive) organisms from the water containing the ammonia.
About source of fish.
Same source... and always the same problem.
Not bashing your LFS but you might need to look into that. Do fishes from them have a good survival rapport among local reefers? Maybe try a different source... maybe a hardier fish. I love blue/green chromies. They are cheap, they school around the tank and are pretty hardy.
Maybe look into your quarantine technique.
Quarantine (QT) is a delicate matter. The overwhelming majority will tell you to QT everything, and it is such a taboo that I see a lot of people outright laying saying they do when in reality they never do (or hardly ever).
The problem with QT is that if it is not done properly you are probably stressing the fish even more than it already is. I have quarantined fish that I bought online (6 anthias), and a couple of fish (neon gobby and scopa tang) from an LFS that doesn't QT. The anthias died while in QT. The other fish survived the QT and made it into my system. I have risked my system by only acclimating fish and then adding them to the main tank. I've been lucky, they survived.
I only remember one case of some type of Ich in my Yellow tang, that went away because its immune system was able to fight it. (I kept lacing his food with garlic... maybe snake oil but he survived)
This is a great article on QTing:
http://www.reefkeeping.com/issues/2004-10/sp/feature/index.php
Don't get me wrong, I am not saying don't QT... I am saying that unless your are doing it properly your are not really increasing the chances of survivability of the fish, maybe even decreasing it. And if your fish are arriving with some type of sickness from the LFS the QT won't do much unless you treat them for it.
Just food for thought though... don't do anything radical yet.
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