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Disease ID - 1st year garden trouble

I started some peppers REAL late, just for giggles, but they've had a real problem lately. We've had heavy rains back to back with excessive early morning humidity, and this had leeched out their granular fertilizer faster than I'd expected; especially in the younger plants with little leaf cover over their pots. They started showing nitrogen defeciency and in the morning the undersides of their leaves were saturated, which lead to fungal/bacterial growth in the youngest plants, with a 3 month old habanero dropping a lot of leaves and the juvenile peppers taking heavy damage. The juveniles I don't mind losing, but I was considering taking it inside for the winter because it has a beautiful stem structure, but I'm wondering if it might even be a seed-born illness that would make the endeavor futile. The other plants I have were either bought from a nursery or gifted as seedlings, only the plants I've started from seed seem affected.
 
TL;DR- Dafuq these plants?
 
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I personally would cut off the bad leaves, get some dry soil transplant them into larger containers with the dry soil and allow the plant to droop before adding any more water or nutrients, keep them from getting water till they wilt/droop and tell you 'we need water' then add a small amount of water only and watch them carefully. I would put them in containers like the one large one you have there and when you add water after they tell you too, use about 20oz right around the stalk (water only)
 
Just what I would do....
 
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