Hi Tammy and Welcome to Reefland!
1. I would not bother with the rock if it has Valonia on it. Sure you can get it off by scrubbing it but you are taking a chance of not getting it all off and introducing it to your tank where it can become problematic.
2. It is possible and most definately and contributing factor. Anything that use filter media or bio-media needs to be cleaned frequently to remove waste they accumulate, if this has not been done it is surely contributing to the nutrients.
3. Do a search for wet/dry and read some of the various comments; the short of it is don't bother with running any type of bio-media in it. Stick with heavy skimming!
4. See #1.
5. See # 2 & 3.
Regards,
Scott Z.



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