Are you in the Southern hemisphere?

Not to go too deep into the issues, I have found that the roots of most plants prefer opaque containers. Also, I try to transplant as least often as possible. I start in very small cells, transplant to approx. a 1 -2 pint cup, then into the final container or bed. For some faster germinating plants like squash, if I don't direct seed, they are started later and then moved directly from the tiny cell into the bed.

Negative, I live in the North West, Washington. Outside of a few months of heat during these summer months the weather is Bi-Polar and unsteady at best.

Opaque container? such as a darker color container not allowing light to pass through it?
Ok. when I was transplanting them, I washed the excess dirt matter around the root systems off with a light mist from a hose in an attempt not to damage the root system. At first transplant the pepper plants were droopy/wilty looking from what I believe to be root shock? but several hours later they perked right back up.

I went from seed pellets, to 9oz clear cups, then once the plants roots started to curl at the bottom of the cup I moved them to 16oz clear solo cups.

Should I jump them to say, a 1 or 2qt bucket next to avoid additional unnecessary transplanting?

In my experience, peppers are 'sun-lovers'. They don't do well in low-light conditions. If you are in the northern hemisphere, unless you are going to grow under something like Halides or Low Pressure Sodium, the longer they are kept indoors - the longer they will languish. If they are going outside, they need acclimation. If going under lights, they need gentle and patient exposure to brighter lights.

Not necessarily a darker color, but as you say, something light will not penetrate. The roots of a good-many plants do better without light.

I stopped using pellets a long time ago... are those peat? Did they have those 'nets' around them? I know some people use them successfully, but for whatever reason (I'm sure it's something I do) I have trouble. However, you should continue using them if you are comfortable with their performance.

Again, this is just my experience, but I think my plants do much better when they go through as few transplants as possible, and I'm not sure there is such a thing as 'excess dirt matter' around the roots. I may be misunderstanding, but in my mind I have a picture of washing off some dirt to put them into more dirt lol.

I try to create as little interference with roots as possible. There are some people who prune roots, but these days I try not to disturb anything unless absolutely necessary. I try to time the transplanting times not solely by above-soil growth or age, but by taking an educated, and somewhat experienced guess at root growth. Making the transition from container to container, to final location as seamlessly, quickly, and uneventfully as possible works best for me... and the plants appear to prefer being undisturbed.

Timing is somewhat important and comes with experience, but as long as you have the space, use containers that will support root growth in time with the plant's needs.

Like I said... for peppers, tomatoes, eggplants, etc... I go from cells, to small pots, to garden beds. Anything more than that and either the weather hasn't cooperated, or I've made a mistake in my timing.

For example... my healthiest plants with the most vigorous starts, are those which I timed to just be at the stage that they are not root-bound at all, but will perfectly hold all the container's medium in a clean, compact shape as they are transplanted. Roots of most plants should be perfectly white (from darkness) and 'clean' looking, with very fine 'hairs'. Again, in my experience, the more you damage those tiny hairs, the worse the plants will fare.

Unless you have some impediment or reason for waiting, if it were me, I'd get them acclimated and into their designated 'homes' as soon as possible.

There's a good chance that whatever is making them perform under-par will be cleared up under brighter light in their prepared beds or containers

Yes i used peat pellets that came with expanding nets around them. I had some issues with them holding too much moisture and several plants had mold grow on the root systems.

appologies for the confusion, I was informed from a friend with previous pepper experience, that when transplanting you should introduce them to a completely new soil body, and to rinse all soil holding the root cluster away leaving just bare roots. Then introduce them to the new soil body. I am not sure how to explain it, I am still learning alot of these terms and have found many people share a large variety of techniques for transplanting.

I see the logic in what you are saying. I think i will slowly transition them to the more direct sunlight and outside temperature. I think I have lots of research to do.
Thank you for your insight!

I see in your list of ingredients that you have bark chips, but while growing in containers in addition to bark chips you should use perlite to allow for better drainage. From the pics it looks like the soil you are using is mostly peat and depending on how often you water it may be drowning those ones that are yellow with leaves dropping.

Thank you for your response Habjolokia.I understand what you are saying. I went and purchased some perilite and mixed some new soil. I had a few plants that were out growin their containers so I used the new mixture with them, this will be a test run. I never thought about the peat mixture to the level you described and see what you are saying now. I will update on the plants response to the new mixture.

They all look etiolated to me. Severely, at that. I'm no pepper expert by any means but clearly, they are all too tall.

I expect peppers seedlings height to be low to the soil, like this:

Zachary, is there a reason these have not been outside in full sun?

With seedlings, unless they are so tangled that you have to untangle the whole thing, I merely tickle the roots to loosen the roots. Normally, the roots will have just about reached the bottom but have not begun twirling on itself. I also make sure, presuming the seedlings were doing well, that their old soil falls into the new pot. Not sure why your friend would tell you to remove all the soil...

If these were mine, I'd start over with most of the ones pictured; some look okay. OR--you could take it out to a 1 gallon pot, half fill with soil, drop the etiolated seedling in up to its neck and cover in soil to the top, leaving only the leaves peeking out. Bury the stem completely. I usually do this after snipping off the bottom set of leaves (for healthy plants) but many of yours do not have any leaves other than the cotyledons.... While doing this, I would not expect much from the ones with only two leaves, have a bit more hope if it has two sets, and any more, you should be fine though there's not too much left to your season!

Here is how I would do it, as a last ditch attempt:

Pinch off the leaf at the red arrow (flush to the stem) and when you pot it, fill the soil up to the green line, ensuring the snipped leaf area is below soil. It will grow new roots from there, if this works. Then put it outside in shade, gradually getting it to full, FULL sun over the next 10 - 14 days. Gradually. The ones that don't even have two sets of leaves like the one behind it, I would toss. But that's me. :) The one in front -- possible.

I'd also suspect overwatering tho some of your cups look bone dry and others sopping wet. The cups do have drainage holes, yes? I noticed the double cupping but also want to make sure you are not letting the water sit in the second cup. The water has to drain--away from the soil and out of the cup. The double cupping also doesn't let the drainage hole breathe either.

And if all else fails, there is always next year! Chin up!

I managed to salvage quite a few of the plants and for about 2 weeks they were doing very well, then in what seems like 2 or 3 days the leaves started showing these dark black and green colored spots as well as what I presumed to be damage from Flea Beatles? I looked up some of the damage done to the plants on the forums and many suggested it may be a fungal infection so I have been treating the leaves with Bonicide Garden Dust, rubbing it on the leaves every few days. As well as daily sprays with Garden Safe Fungicide. So far the dark spots on the leaves have not cleared, not have they spread further though. However the new leafs that keep growing are curling and almost drying up within a week of the new leaves starting.

They get approx 8-10 hours of sun a day in the location they are at now in my backyard and I only water them when the soil is dry more than 3 inches into the soil. They are also in 1/2 gallon bottom draining tubs now. I will include some pictures of the current state. The current moisture on the leaves is from a dose of fungicide3 spray by Garden Safe.

I grow in peat pellets. It's hard work and lots of patience. I do have much better success with a 50% or less potting mix. My favorite is Pro Mix but it's expensive.

Second thing growth on roots a really bad thing. Let them dry out. Then water with about a cup of peroxide to a gallon of water it will sizzle but that's ok. The reason for that is the "nightshade" family does not for bonds with microbs like members of the lentil family.

Third I have never used the expensive lights to start seeds. But it does take a lot of light and the right kind of light you need blue on the Kelvin scale. Usually you can find daylight bulbs for the right color 5000k-7500k a few of the red bulbs is ok. Now if you want to grow indoors then you need a lot of red some blue green and yellow. I use regular led and CFL bulbs to great success.... when I can get the temperatures right on the fruit set..

Chlorosis or yellowing of the leaves and or plant can be caused by those conditions discribbed above along with mineral deficiencies including nitrogen.

I think those are to small to top. Most people I talk to say the leave the first row of true leaves and way for the coyotes to fall off or at least start.

That mix looks like 5-1-1 mix... I love that mix but in truth I add a small amount of my natural clay for mineral support and water retention. I also like the very cheap "top soil" from the sand and mulch place. It's just sand and real compost unlike the commercial compost that is already spent. Spent meaning most of the nutrients has been sucked out.

I hope this info will help you in both your current and future endeavors.

Thank you for the words T S. Being still new to this kind of plant growing I am unsure what the whole 5-1-1 mix means, but I can say that since the last update, my plants are doing great! I was able to troubleshoot the spots/ white growth on the leaves to a fugal infection the plants were being plagued by. I put them through a series of bug and fungal treatment sprays and chopped off the effected leaves to prevent it from spreading and I am now left with a decent more healthy looking plant.

My next question would be, has anyone heard of topping pepper plants? Out of habbit when these plants were still very young I topped them prematurely and I believe it might have been part of the problems I had. When should I "top" my plants?

The pictures below are my plants in their current state.