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Stem rot, should I pull the plant? (pic)

It may be some sort of deficiency, but it looks like there's new growth on it. How does the plant look, overall? May be treatable.
 
All the plants were doing great, they are in earthboxes, weather got very cool here in NY for the last two weeks and all the new growth started to curl and wrinkle.  Landscapers were rampant around here spraying 2-4,d at the end of May, tomato plants were affected right away. So many things going on.  This problem seems unrelated, when it happenned before all the leaves on the stem wilted and I cut off below rot.
 
  In your zone you may need to evaluate weather your going to be able to ripen pods in time,I live in Iowa a have gave the boot to 8 plants that were lagging for one reason or another.Replaced them with quicker peppers or Toms.
 
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