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It really depends on where you live, but most peppers can be planted outside after your area's last frost date, and those indoors should be started at least 6-8 weeks prior to that.

You are too nice to them is why they have thin skin. Plants develop thicker skin to help protect them from the elements. I would guess that where your plants are growing is sheltered from winds and harsh sun. While I have not tried this personally, I am guessing that since reducing harsh elements on peppers makes their skin thinner, increasing it will thicken them. Try giving the plants a gentle shake every so often to trick them into thinking they are in a windier environment than they actually are. You may also just be growing a thin skinned variety but the technique above should work for them too.

This article will help with that: https://www.gardeningknowhow.com/edible/vegetables/pepper/pruning-bell-peppers.htm

I would not snip off the bottom leaves on any plant. The cotyledon leaves (the first leaves) fall off on their own and snipping them off puts undue stress on the plant.

Bell peppers often have a purple-black coloration at points where stems meet, but if the black color is a solid black and the area is shriveled, this would indicate the black are is the issue. One thing that I can think of that could be causing the issue is a condition called stem scald, which normally happens on the main stem. What happens is a heat source can focus heat on a part of the stem and it wilts. It is known to happen when plastic is used and it focuses the heat onto a part of the stem. Here is more information: https://www.gardeningknowhow.com/edible/vegetables/pepper/black-stems-on-pepper-plants.htm

I would have your soil tested at the local extension service. While you are adding manure, it normally only adds nitrogen and you may be deficient in one of the other macro or micro nutrients the plants need. If I had to guess, I would say it is likely potassium you are low on, but a soil test will tell you for sure.