Full disclaimer: I haven't read every post up to this one. Redundancy possible.
First I should say that the images don't indicate root rot to my eyes. Roots would be coated in an obvious slime and they'll slough off easily. Give a root bunch a very light tug. Root rot usually develops thick and fast. The plants do look a little burned and slumped; I would recommend reconsidering square one and rethinking environment (temp/humid/light distance), ph/water quality/source, nutrient concentrations, etc, and see if you missed something there. Check your notes (keep notes!), any big swings lately? Plants don't regard rapid changes well, usually. Also remember kelp based and/or humic acid additives will harmlessly brown up your roots a bit (e.g. Adv Nutrients B-52 will do this).
If it is indeed root rot, I'd caution you by saying that turning a 'live' system to a sterile one and then back again to live can be a gamble. What usually ends up happening is a brief period of no problems, then a surprise return of the root rot. Thus dramatically extending the time under duress of the plant. Once you clear it up with H2O2 (or sodium hypo, et al) I would heartily recommend you complete the plants life cycle in that new sterile setting.
MM