I am not sure what critters were under the pot, there are many harmless ones that would be attracted to the moisture and sun protection. You can place the containers on wood/brick pieces to elevate them an inch or so off the ground to get rid of them. If it was the bottom most leaves that fell off those were almost certainly seed leaves and it's normal for those to be cast off some time after true leaves form so no worries there. Cukes grow a lot faster than peppers so I wouldn't be too concerned about them in this case. It takes a lot more predation to bother them than the slower growing peppers. Probably a good time to head to the store and replace the peppers that are just stems. If they survive then you have bonus plants :) In the case of the disappearing leaves or half gone leaves I would be looking for a pest as the culprit. May have already moved on, if you are lucky.

I agree that you should get rid of the weeds and fertilize. My Sweet Cherry peppers seemed stunted too. After transplanting, the plants more than doubled their growth and each put out about 3 peppers. Then they seemed to go dormant. For about a month or so, there was no growth and no more buds. My solution was to fertilize weekly with water soluble 10-30-10 fertilizer and every two weeks to give a dose of Epsom salts, either 1 TB sprinkled at the base of each plant, or foliar feeding with a solution of 1 TB of Epsom salts per gallon of water. This treatment really worked and the pepper plants are loaded with new flower buds.

Without doing a soil test, you won't know if you have to my Nitrogen. A way to make plants seed/fruit is to stress them. My neighbor stressed her plants with the lack of water and they went to fruit. All the fruit were small, but there are reasons behind it. She didn't mean to stress them but when you plant with a larger of cardboard and a few inches of top soil on top, you have to water non-stop. She missed a day and everything started to wilt. When she got back to watering, within a couple days, everything had flowers on it and started to fruit. As to the reason her peppers and such are small is because she really needs to water twice a day, and she still misses some days. Good luck in getting your plants to fruit... BTW, here plants went to fruit within a couple weeks from planting. I planted a week or more before her, and mine didn't start to fruit for a good 3 or 4 weeks after her's. I've got 3 or 4 peppers per plant now and have picked a couple of good sized greens already.. Basically I could pick a full sized bell pepper ever few days and have plenty.

Well, since no one here had a suggestion, I bit the bullet (Felcos?) and cut down the bald branches. No green inside (whew!). But there are other branches from the same plant with all their leaves, just beginning to fruit. I'm guessing it was either some sort of disease or the cycle of the plant--after a few years of blooms, it's time to prune off branches that lose their leaves.