Brown roots in hydro means you've got algae growing in your reservior. No good. Light should not be getting to your water at all. I suggest you change methods to DWC using black 5 gallon buckets and black lids, to minimize the amount of light getting to the water. Also, varying your nutes like 2 oz here, 40 ounces there, probably isn't a good idea. In DWC usually around 1000 ppm works pretty well, lesser when they're young and raise the ppm over time to a max of about 1100 ppm or so. You'll have to experiment a little and see how they do. Give less to start with and if they look light green or yellowing, chances are good you can raise the ppm some. Once you find a nute amount that works, stick with it. There's nothing about nutrients that will make the plants provide a greater effect upon use. In DWC, they will grow quickly and abundantly if done right. I think your ppm as it is, is too low, but your brown roots indicate algae growth, so if you want to stay with flood and drain, you've got to clean the res and tubing and everything, with some bleach/water mix. Just dump it down the tub when done. DWC requires either small air pumps for each bucket or a larger one that will provide enough air for all your plants.