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Couple of begginer questions

Hi all!  I've been a lurker for a few weeks, new to growing peppers.  I harvested cherry pepper seeds from a local farmers market pod last year.  I have one overwintered plant from last fall I started from seed and a few seedlings I started around April.
 
The overwintered plant started growing fruit few weeks ago.  I have some brown spots on a young pod and don't know the cause. Normal?  Bacteria? Something taking a nip at the pod? 
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Others pods are smooth and normal with no spots.  Pods are pretty small, but this thing is in such a small pot.  Since this has been outside in late May, have had ants, TONS of aphids, and maybe even white flys on this plant.  After seeing the spots and bugs, Sprayed with Bayer Natria spray (the one with 10% sulfur something)  and seems to have taken care of the bugs.  Will spray again in few days as is always suggested to stop lifecycle.
 
Also, I think some of my small plants I started from seed ready to transplant into the garden are dying.  I was hardening them off outside and we got a few days of heavy rain and I could tell they were severly overwatered or affected by pests.  The leaves like folded in half.  They were already in full sun all day before this happened, and returned to full sun after the rains but they developed brownish specs and mishapen leaves.  They are still growing but very slowly and look pretty bad, with the mishapen leaves, and burnt looking tips on some leaves.  I've also had to spray these a couple times with soap/water solution, then the Natria a couple of times because of all the bugs that keep coming back to them.  Is it a fungus?  Are they goners?
 
Potting soil = 1 part CoastOfMaine lobster compost, 1 part vermiculite, 3 parts MG bagged garden soil.
Temps = 50-60F at night, 70-80F day, Full sun
PH = Have a cheap electro meter but haven't taken it yet.
 
Thanks for your time, appreciate any help.
 
Overwatering:
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Brown:
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Too me everything looks bacterial which can be from too much water , I would ease up on the watering or get a soil that holds less h2o. Remove any leaves that have brown spots and spray with 1/2 skim  milk 1/2 water solutions once a week until it is gone . 
 
Yeah...I am with Jamie on this one. Too much water/poor drainage on your little containers. Even in CT it is about time to put them babies either in the ground or into some larger containers for the year. If you are going with containers choose a good soil...browsing the site will give you many recommendations for good soils.
 
As far as the little specs on your pods, I wouldn't worry. That may be some insect damage...or even just a normal occurrence like corking on Jals. 
 
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