Need help pruning

So this is my first time I've ever wanted to keep a plant alive. My wife got this thai chili plant(I think) for my birthday last year since I love them so much. And it survived the entire year. Surprised to see a plant still living over half a year under my ownership, I decided to dedicate more love to it this year to make sure it keeps giving.

What I did already was use some food-safe plant food and worked that into the soil. I then pruned all the obviously dead stuff, the obvious stuff like diseased/dead portions, small branches near the base. Now I'm wondering about these flowers. I've read that the peppers grow from the flowers after they bloom, but I also heard you should prune them to reserve nutrients for the roots. I still never transfered this to a permanent pot yet but it seems to be doing fine in the original monrovia plastic pot for now. I'm guessing that the roots on this bad boy are well established by now, right? Would transferring to a slightly bigger pot shock it?

Back to the main point, in the pictures you can seeplenty of flowers blooming and some already dying with the peppers beginning to sprout from them. In the first picture if you look closely in the canopy, there are two quarter grown peppers with a lot of black on them. Are they burned and should be pruned or are they worth saving and the black will go away?

Most of my experience with plants is weeding and pruning the very obvious stuff like what I've already done. Dont know much about the dynamics of pepper health and what healthy stuff is good to prune for the sake of the rest of the plant. Any and all help is greatly appreciated!