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The best way to diagnose gill flukes is to look at the gills of the fish with a magnifying glass. Check out this site.
http://www.geocities.com/steevward/dactyls.html
If they have flukes dip them in 10ppm Potassium Permanganate for 10 minutes.
My feeling is that they do not have flukes but there is something causing a drop in the oxygen content of your tank. I'd jack up the aeration in your tank to the max., fast!
 

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I'm not sure there are any really good/reliable tests for CO2. What I do is just add a fixed amount of CO2 to my tank each morning.
As far as Flourish Excel, I stopped using it because of the human toxicity. After reading about the effects of gluteraldehyde on humans, I began thinking that some of the alergic problems I was having might have been exacerbated by Excel. Not scientific but why do I need any more chemicals in my life?

I'm happy your tank is back to something like normal. [-o<
 

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You can use Excel with CO2 but I don't recommend it. If you are using CO2 Excel is a waste and adding extra chemical to your tank.
I don't think there is any good way to know how much CO2 is in your tank except by what you put in. I add a fixed amount to my tank each day and check the pH and TDS frequnently.
 

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Excel/No Excel

Sorry to disagree with Ray but you can safely add Excel and CO2 to a tank without issue and I do when doing water changes and when starting up a new tank or scape as the Excel helps knock back any algae in the tank. If you have good CO2 levels then you don't need to add it every day.A.
Excel is a polymerized form of glutaraldehyde and its effect is a result of it breaking down to that compound.

Here are some references. Decide for yourself if you want to use it our not.

http://en.wikipedia.org/wiki/Glutaraldehyde
http://www.cdc.gov/niosh/topics/glutaraldehyde/
 
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