Ok, here are the recent pics of the clones that were experiencing the deficiencies earlier. They have healed a lot since the transplantation and I have given them nothing but 6.5 pH'ed water after the flush so the verdict is: Root bound causes deficiencies. Nutrients for clones at 1/4 strength during their 3-4th weeks is not recommended.
As for the flush, I used half the recommended dosage as suggested on the Fox Farm Feeding Schedule and went 1 tsp/gal with the Sledgehammer then flushed again with clear pH'ed water.