1. Why would you let clones sit in the dark for any period? Generally weak light is where they should be kept. Never in the dark.
2. After just a few days the cuttings need more fresh air, less humidity. TOO HUMID/MOIST.
3. You obviously have a deficiency going on. At first it looked to me like an Mg problem (yellowing at new grow points) but it could actually be a number of things. You should be adding some mild bloom fert at this point- maybe a 25% solution.
4. I have found there are 2 mains points with cloning: 1) some strains do great and others don't. Some put off roots in just a few days, others can take 10+ days. Just genetics I'm guessing and 2) choosing the right cloning material. I stop giving N at week before the cuts are taking, and mist down the leaves daily (to help drain N out of the plant)- this helps stiffen the stems and they are stronger during the early clone phase.
Hmm so many answers to all of your questions...
1)I leave my clones in the dark because that is more conducive for the plant to begin producing root cells.(you can research the chemical and photosynthetic reaction that a plant's cellulose structure has to light retardation/starvation)
2.) After 3 days I open the dome every 3-4 hours (as stated above) I breath on them and re-mist the dome.
3.) The obviousness of my deficiency ( I assume you mean the mother plants that these 4 strains were taken from) is not so obvious. That light green that you see (only at the fresh growth points mind you...) is actually a sign of new growth before it was taken as a clone. I could post pics of the mothers if you like, but they are all a beautiful green color, and the last thing I would do with a rooting clones is shock it with any kind of nutes. Other than maybe a very very very dilute mixture of seaweed emulsion, but not until they are 2 weeks old. These cuttings are 6 days old right now, and every one of them are springy and standing straight save 1, and the 2 that did not survive.
I believe that you are correct about the sensitivity of certain strains to the stresses of cloning, as I am only having trouble with Chernobyl and Royal Kush... Ny Diesel, Ny Sour Diesel, and my DICE have all been no problem to clone. The Sour diesel I took clones from a budding plant to keep the strain going and they are doing magnificently. I also managed to successfully clone a budding Chernobyl... so again I am confused as to exactly what I am doing wrong. I will try a dryer approach this time and see if that doesnt help.