Well, first off, very nice job so far. Plants look great.
Couple comments. As far as your root rot goes, I would say it's in the early stages and still very fixable. I add about 30 ml per gallon (so 180 ml for your whole res) of 3% hydrogen peroxide whenever I see the first sign of rot.
A Couple steps to prevention. Stop letting your water sit out. Any chlorine in the water will dissipate within about 30 min in your tank. If you can taste the chlorine in your water, go to a pet supply store and get some fish tank water adjustment drops for when your starting a new aquarium. That should take quick care of it. Stagnant water is no good... your letting it fill up with all kinds of mold and bacteria floating around in your house. pH adjust the water to 5.8 then put it in. Step two- More bubbles, add an extra airpump and airstone or three and your water temps will come down to the point where pythium (root rot) won't be a problem. If that doesn't bring the water temps down to about 65 then add frozen water bottles throughout the day till you can add enough air to the water or bring the ambient air temp closer to 65 continuesly which would keep your res temp a little cooler (with the added air).
Oh and your plants look a bit streched, you want those lights within a couple inches of your plant. You should be moving them everyday. Good luck Bro.