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Use clean garden tools to prune your pepper.
Remember that the branches can break easily so handle the plant carefully.
Remove any dead, diseased or damaged stems.
You can thin the plant as desired to open up the canopy.
Clip the ends of branches as needed to keep maintain a good shape.
If the plant is heavy on one side, trim to maintain balance.
You can watch for blossoming, if branches do not produce flowers, they can be pruned away to keep energy on pepper formation.

Stake you plant to support it's weight.

https://www.gardeningknowhow.com/edible/vegetables/pepper/growing-ghost-chili-peppers.htm

Chillies are surprisingly sensitive to temperature and water changes which can affect flower/fruit production. Try a high potassium fertiliser. This will help improve the plants resistance to temperature and water fluctuations.

There are some specifics needed in care to grow Ghost Peppers.
The fruit are quite delicate, so your description of soft seems right.
I do want to mention that in my research, I have found numerous reports of people purchasing seed that is represented as Ghost Pepper seed, and that they are not either of good quality or not Ghost Pepper seeds at all.
Make sure you purchase from reputable sellers.

https://www.gardeningknowhow.com/edible/vegetables/pepper/growing-ghost-chili-peppers.htm

Peppers are sensitive to rot, so I would not cover them. These will be easier started indoors in cell trays. They will need bright light, but you can start them under an array of CFL bulbs, or even LED's. Just don't use regular incandescent bulbs. They can even be started in a window that receives Sunlight all day.

Just spray when the soil starts to dry. Keep it slightly moist at all times. It doesn't need to be wet, or completely dry.

35 day germination means that it can take up to 35 days for germination to start.

This is a severe fungal infection. You are going to want to go ahead and pot that up into a larger container with fresh soil. Make sure that the soil is not infected before using. It should smell like soil, but not rotting, or like bread or alcohol.

After potting up, make up a mixture of 1/4 peroxide, and 3/4 water. Water this once, and it will help to take care of the infection.

Make sure that you are not overwatering. If there is any moisture at all within two inches of the top of the soil, then you will want to wait until it is completely dry down to about two inches. Overwatering is the most common cause of this issue, so it is important to only water when necessary.

I grow serrano peppers and I don't prune them at all. On the other hand, they are in containers with a plant support around them. Stem breakage has never been a problem for me and production is heavy. The idea behind pruning peppers is to have sturdier central stems as some larger varieties are prone to breaking. On the other hand, producing fruit is very taxing for a plant - it takes a lot of energy. More leaves = more plant energy. The following link discusses pros and cons and has a video on how/when to prune. Gardening is an on-going learning experience and experiment. https://www.therustedgarden.com/blogs/vegetable-gardening-tips-blog/how-to-the-benefits-of-topping-off-or-pruning-pepper-plants-several-video-examples-with-control-plant