Thanks for the feedback..I will continue to post updates and pictures. I hope I do not have root rot! I am going to post in the problem plant area with some better close-ups on the roots.

As far as the lighting OP, that 400w HID is going to be in a closet that is roughly 7' x 2.5', and my plan was to just have an oscillating fan inside the closet. Do you think that a closet this size will require better ventilation? If so, any suggestions? I had not thought of this yet...

maybe I should go for a lower wattage HID?