Your doing a great job at diagnosing the problem. One change at a time. Keep doing it like this. I don't ever trust RODI water from LFS. It's shady they say it's good but you don't know if you don't test. I would go on Amazon and get you a TDS meter the cost is minimal for the use you'll get out of it. It will pay for itself in the first use.
http://amzn.to/2qPX0YX Here's the one I use. I bet you get a reading of 9 or higher from the LFS water. If so that is a part of it. Second try putting some pods in. They can help clean up the waste a bit more. Third what kind of rock did use? Lastly if you have an open spot some where put a hand full of Seachem matrix or pond matrix in a bag for extra biological filtration growth. Keep changing one thing at a time though until the problem is solved. I feel the water is the factor, but your skimmer may solve it as well if it was dead. That will take a good 2 to 3 weeks to see if that is the solution first so it can start clearing the water column out. Good luck man.