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Leaf or Bacterial Spot? Help needed!

Hi All!!
 
This is my first post so ill give you a quick intro.  This is my first year gardening.  I have raised beds with soaker hose irrigation.  I have tomatoes, beans, jalapenos, lunch box peppers, banana peppers, habs, chili peppers, and onions.  I composted with mushroom compost before planting in late march.  I fertilize every two weeks with Jobes organic 2-7-4.
 
All my plants are producing fruit. I have started to notice these spots are more prevalent on my lunch box orange peppers and bell/chili peppers. We had about a week of straight rain in Texas, followed by 90 degree temps this week. The fruit DO NOT look affected yet. I am trying to nip this in the butt. I just ordered chlorothalonil. Not sure if it will work or not. Any help or advice is appreciated.
 
FYI:  my jalapenos look great.  Habaneros are decent, they got hit with aphids early in growing season but seem to have recovered.  
 

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Any outer leaves or new leaves affected?  If mostly the bottom and old ones I would say issues from the moisture/rain.  That happens to me every year and they always grow out of it.
 
Ill have to check.  Ill get some pictures of the infected today.  I want to say its on all the older leaves.  I definitely have a worm problem, as I found couple holes in the peppers (and a worm living inside of one!!)  They mostly eat the leaves of my bush beans.    I treated with DE so hopefully that helps.  I tortured a worm with DE and it didnt seem to have much of an affect on it though.  Hopefully it just takes some time to kill them.  
 
thanks for the reply!
 
I can get behind what millworkman posted. Right after I filled two beds and watered down I got hit with a thunderstorm. Same look at the bottom leaves. Clipped and let the bed rest, problem ran itself right out. 
 
I have the same thing on some of my smaller plants that I haven't transplanted and moved down to our Pecan orchard. we had over 10" of rain down here near Galveston these last few weeks and the ones here at the house got hammered. The larger plants I have moved already to the orchard and are under the canopy the mature trees have look fine. 
I have removed the leaves that look bad and already see new growth so they ought to pull out.
 
Thanks for the replies.  The plants have pulled through, but my tomatoes are so big and not caged properly so they are stealing some sunlight from them now.  Not sure how much more they will produce.  My first grow, so next time I will be more prepared for this and buy some Texas Tomato Cages.  Tomatoes are easily 7 feet tall.  
 
Here are some other pics to keep you interested:
 

Also, notice the tops of my hands are stained in last photo.  I have no idea what that is from.  I have been using DE in the garden, but do not think it is that.  I pulled a bunch of bean plants out, but I had gloves on i think.  Been about two weeks.  Any ideas?  It wont come off but I havent tried any type of concoction yet.  
 

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