Kleeem
You mentioned that your reservoir reached the 90's, what is the normal temp of the reservoir? If the normal temp is to high then the roots may be suffering from prolonged heat. That will give you brown roots also. I attached some pictures of my first experience with high
nutrient temps. Those roots were subject to prolonged 90 degree water temps, 68 to 72 degrees is optional for roots. Warm water temps will also provide better conditions for some pathogens to breed and multiply.
Cleaning the system thoroughly with bleach should work, but it needs to soak for a while first to do the job, at least 10 to 20 minutes or so, I like 30 and longer myself for sterilization. Also you need to be very thorough, sterilizing every nook and cranny of the entire system, not only the reservoir and growing chamber, but including all the tubing, baskets,
growing medium, pumps etc.. I will wash everything thoroughly with soap and water first then sterilize after that. I also wash the
pump with soap and water, as well as the main tubing and reservoir with every nutrient solution change, just to keep any pathogens from getting a foothold (it only takes me about 10-20 minutes).
A couple more things to consider is water and air quality. Pathogens can also be introduced into your system through water and air. I know you mentioned that you rinsed with RO water. RO water should be free of pathogens when it first comes out of the tap. But if it's stored in another container before it's used, that could be a source of a problem (if it's not regularly cleaned). It's imposable to keep pathogens out of the air in an outdoor setting, but if any debris like dead leaf parts, small twigs and even just dirt/dust is introduced into the system, that's also a source of a possible problem. That can be easily and cheaply remedied.
Another thing to consider is if you are using soil grown plants and washing off the soil to put them into the hydro/aero system, that could be a source of a possible problem as well. Soil born diseases/pathogens can be introduced to the roots at that time and don't wash off, then breed in the hydro system where they then can affect all the rest of the plants in the system. Some plants are more susceptible to soil born diseases/pathogens than others. Strawberry's are one plant that I know of that are very susceptible to them.
Lastly the use of air stones in the reservoir will also help keep some pathogens at bay. And H2O2 (Hydrogen Peroxide) will help kill any pathogens as well. Just the regular 3% H2O2 you get at any pharmacy or in the first aid isle at the market. There is a whole debate as to weather there is stabilizers in H2O2, but all you need to do is read the label for both "active ingredients" and "inactive ingredients" to tell if there is anything else in it ( if that's a concern for you). I have yet to see one that has anything other than Hydrogen Peroxide and purified water used. If purified water is on the label anything else will be as well. I use 5mL (one teaspoon) per gallon of water a week in my systems. You can use more, but it isn't really recommended. I have used 10mL per gallon at times and didn't see any negative effects, but all I can say about that is use your own judgment. Small plants, and especially seedlings tend to be more sensitive to H2O2, thus would show negative effects first.