Transplanting boo boo/Move from passive perlite system to active aero hydro

So I'm in day 38 of my flowering cycle. When I looked today under cfl light I noticed that the leaves were dying and a lot of un healthy leaves. I thought at first it was a salt build up due to the passive watering system. I decided I would rinse the medium and roots off. The medium was perlite, however when I rinsed, the perlite shifted and disrupted the roots a lot. I looked at the roots and noticed they are tanish, not really white like they used to be. (Maybe some decaying material caused some root rote, not sure)

After the major disruption and noticing the roots I decided to transplant into the aeroponics system I built. I had less then an hour to move the 4 plants. I rinsed the roots as careful as possible and lightly shook the roots to remove excess perlite. I moved the plants into 5" net pots. I added the adjusted ph water (5. and added the week six cycle for the nutes and h2o2. The timer for the aeroponics system is 40sec on and 160sec off (2min 40sec off). The light cycle is now off, and I'll be going in tomorrow at 7am.

Has anyone done something as stupid as me? If not or if so, does anyone have any suggestions or things to look out for? If you need more info about the grow, please see my signature for more info.

thanks for constructive comments and ideas in advance.