My two cents...
Too big of pots...
Too much water...(for the love of God, don't flush anymore...this is not the correct way to fix your issues)
Lack of light at the bottom of the canopy...(lollipop your girls and clean out all that larf...the top flowers will thank you later)
The rust spots most likely indicate a Ca issue...
You're nearly 6 weeks into the deal now...slow and steady wins this race. Don't get excited and start throwing the kitchen sink at these things; you're not that far off. Bring them back to some normalcy. Regular feeds in a regular pattern. Quit chasing your tail with the flushes and the runoff checks. Know what you're putting in, what you started with, be sure of your feed / water pH and the rest will take care of itself. Good luck.