Cryptocaryon irritans ( literally means irritating hidden kernel) is a bad parasite but knowing it's life cycle allows for a reliable plan for treatment and some piece of mind. Understanding it is the key to either eradicating it from your tank or atleast living with it at subclinical levels in your aquarium (like nature). I find the closer to a natural diverse reef your system is, the less likely that an introduction of cryptocaryon will establish itself.

Please have a look at this article. It is the best one I have seen.

http://edis.ifas.ufl.edu/fa164

If you are still confused ( or too lazy to try to read the article) I will paraphrase, summarise, and emphasize a few points here that I don't think are apparant in most internet articles. The signs on the fish are often obvious ( white salt grain like spots) but may look different on specific species. OFr example, they may look clumpy and mucoid on a puffer fish and cause the fins to be cloudy wheras on a tang they are precise pinpoints of white when in low numbers and cause a general cloudiness of the skin at higher infection levels.

Ideally you confirm the disease causing agent, cryptocaryon irritans, by microscoping evaluation.If you have access to a microscope and slides, you can scrape a cover slip along the skin or over a fin of an infected fish. Puffers, lions, and clowns are slow and enthusiastic dominant eaters like angels and tangs are gullible to swim into a clear tupperware (see catching fish in tanks section) so don't make excuses. Put that coverslip on a slide and even on 10x objective its an easy diagnosis. Compare to pictures in the aforementioned article.

Lifecycle: The parasite sits on your fish for 3-10ish days, then falls off and grows as a cysts in the sand for 3 days to 3 months (usually around 10 days). Then each cyst sends out 200 infective babies which search for your fish for 24 hrs before either attaching or dying. This is the susceptible to medicine part of the life cycle. Usually you only see the cycst which have been on teh fish growing for a few days already and so once you start treatment meds, all of the newly attached parasites still will grow out and continue to cause disease on the fish until they fall off naturally. Assuming it is crypt, there are a number of ways you can beat it and a number of ways you can try to live with it.

Because it has a complex life cycle including a phase where it falls off of the fish and into your substrate, you can simply remove fish from the tank for up to 5 months (if you are really thorough) but more reasonably 2 months with your tanks temp cranked up to 82 (to speed up the life cycle). Nobody knows better than I do that this is easier said than done.

If you can catch your fish and begin them in a quarantine system, an easy longer term drug to use is copper (cupramine by seachem is easiest) and the salifert test kit is the only one worth buying for monitoring levels. You could use media from your tank to "fast" cycle an empty 55gal tank or even 50 gallon tupperware with even just a bubbler/spongfilter but better a hang on tank aquaclear or something. Another wild way to rid particular fish of the disease is what is called the tank change method. It involves moving infected fish to a clean quarantine tank every two days. This makes it so that the cysts fallinjg off dont have time to grow and send out babies. For your puffer for example, move it to a 5 gallon bucket with 1 gallon of aquarium water and add 1 gallon of makup water to it an hour for 3 hours (to dilute any infective stages and increase water quality). This removes him from continued infection by those babies. At the same time take out 4 gallons of tank water which you wilol use in teh next days as water for the buckets you will move the puffer between (seperating the water from teh tank means that the babies swimming around will die within 24 hours and you will have nice tank water to move the puffer into without parasite). The second day move the puffer to a new 5 gallon bucket with 2 gallons of water from the bucket of tank water you seprated yesterday and 2 gallons of makup water. the puffer will live in here for 2 days then you will do the switch again. To reduce chance of ammonia toxicity you can put a few drops of prime or amquel to detoxify ammonia each time you move the fish. In 10 days the fish should be clear. This is a rough and tumble way to fish the problem but the idea can be modified to use 20 gallon tanks/tupperwares for 5 fish at a time etc. Something to realise is that the parasites on the fish are still causing trouble until they fall off. The ones we can see (look like slime/salt grains/ or fluff on different fish) are the older ones but there still is smaller (1-4 day old ) parasites coming up through teh ranks which may cause secondary infection and osmotic problems (they break down the fishes ability to keep saltiness out). Often with treating ich I run a secondary antibiotic like nitrofurazone (which anecdotally also breaks the crypto life cycle but isnt discussed in the literature). Some fish are more resistant in general to crypt (wrasses/mandarins) and over time fish do develop a partial immunity to it, however when it is ramped up, as might be the case in your tank, it is a game of statistical challege and atleast some of the thousands of infective stages will get through. Living with crypt: I've seen many reef tanks just live with the parasite subclinically and present as a spot on a tang every so often. I believe this is because things like hermit crabs and sand sifters actually eat the cysts. I have a quarantine room and keep a juvenile spanish hogfish as a loaner fish to friends who let crypt into their tanks as this little fish actually aggressively picks fish with the parasite clean (exept for the parasites in the gills) and keeps the burden low enough for a while that the fish may build a resistance. Some cleaner shrimp (blood/skunk/coral banded) will do this too and even baby pomacanthus angels (french/emperor) but it's hit or miss. Neon gobies generally wont clean crypt but I have seen a few big ones do a good job. Here is a link to youtube showing the parasites at what looks like 200x.

http://www.youtube.com/watch?v=aoygJCo0gco

I  know the frustration of having a disease and not having anyone able to help immediately. Some of these ornamentals are fragile and die fast. I recently lost a moorish idol in quarantine within a day from when I saw symptoms and diagnosed this parasite. It's possible something else was wrong (bacterial/viral) however this fish was eating and had no other symptoms than the spots and rapid respiratory rate that morning.