Waste does accumulate in gravel. My gravel, however, is perfectly clean with the help of my school of catfish. As for nitrate/nitrite levels, you may consider a freshwater clam to filter out the nitrate. If you don't already have a biological filtration system such as Emperor Bio-wheel, you should get one. These eliminate nitrites on contact, and are really powerful. I have one, and I haven't ever hade a problem with nitrites/nitrates in months. pH is less costly than the others. Go to your LFS and ask for Acid buffer for a 110 gallon tank. If all that's available to you is walmart, and petco, instead of asking the inexperienced people there, try Seachem Acid Buffer. That's what I use, and It maintains pH for a long period of time. For gravel, use substrate that water can flow through well. Aquarium salt seems to forever lower the pH for some reason in my tank. I try to raise it to 6.8, but it keeps going down again in an hour!