First off, the flooding should not have adversely affected your plants. The water should have been well oxygenated and would not have caused rot. If your pumps run at a regular cycle (day and night) the pooled water at the bottom of your tray will be beneficial to your plants, not be a source for rot. Stagnant water is the enemy, fresh flowing water is not. Stagnant water is easiest to detect by its horrific odour, usually combined with a filmy skin.

Now, rockwool cubes. These things are a perfect breeding ground for mold and algae. The should never be exposed to light and should be completely submerged during the flood cycle (or conversely, never submerged in the first place) to wash out nutrients and such.

Roots, in my experience should be a bright white colour. Darkening of the roots is usually indicative of death or illness. However, tan roots may be a genetic trait. Perhaps, someone else could clear that up.

As for you leaves, the plant pics look like the starting stages of nute deficiency, but the pic of the single leaf looks like nute burn. One of the Plant Doctors on duty would most certainly give you a better opinion.

Good luck.

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