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Welcome to the forum!

It is ok to do water changes in a new tank, it will only remove some of the ammonia to protect the fish from high levels. To much water change will slow your cycle though so I wouldn't change more than 10% twice a week unless you need to control the ammonia. Anything close to .25ppm is very bad and water changes will be needed to control it.

With the ammonia, it could acutally be something else than ich but it doesn't rule it out. It sounds like the fish could have had ich from the LFS which happens a lot unfortunately.

Keep an eye on the ammonia and keep up with water changes, in the future, you can cycle without fish in about a month.

Here is an article I compiled from experience and some really good aquarium keepers about the fishless cycle for future references. http://www.fishforum.com/viewtopic.php?t=3738
 

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Ok, that tells me that it is not cycled yet, possibly. 0 nitrates means they are not being produced yet by the bacteria needed to handle them. It could mean that water changes are kepeing them down to an unreadeable level but I would keep testing my ammonia for the next couple weeks to make sure.

As for the "spots" are they all the same shape and size? Do they have a distinct shape to them or are they just an odd shaped "mass"?

A very detailed description of the spots will help to positively identify them and what they actually are. A picture would be even better but that is a difficult task in itself.
 
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