Hi Jimdog! Congrats on the DIY box project and so far working out all the issues of heat and light and airflow. I agree with your wife that you need to go to flower sooner than later, your problem will be the plants getting too big and too tall to live in that box... especially with that many of them... but I assume that half of them will be culled soon as males.
The one with the funny leaves at the top, it looks like what happens after a FIM... did you try Fimming that one?
The deficiencies that are showing up in the most robust plants might very well be indicating that they are becoming rootbound and the root are having troubles uptaking nutrients. Have you tried popping them out of the present containers just to look at the roots adn see if they are wrapping around the outside?
The one picture with the hole in the leaf concerns me too... unfortunately being sort of outside, you are also susceptible to bugs... and it looks like you have one in there that likes munching on leaves.
Lastly, part of your deficiency problem does seem to be possibly pH related... I am seeing the start of a specific deficiency, but hard to tell at this point just what it is. As Kraize asked, do you check the pH of your water and water/nute mixes? Now that you are growing in a container and not outside in the ground, pH is an issue that you need to keep within a specific range.
In summary, I think I see a nitrogen deficiency that more than likely is due to root wrapping... it is very easy to get nitrogen to plants across a wide pH range... so usually this problem has to do with root problems or watering too often. You say that you water every 3 days... so that sounds like you are drying them out properly between waterings... when you do water, do you soak them completely and produce run off?
The other problem looks to be pH related and possibly the start of a calcium or magnesium deficiency on one of the most robust plants... and I assume the others will soon join it, since they are in similar situations. Our plants need a lot of magnesium, and to get it up into the plants the pH of the liquids needs to be at 6.5 or higher. We know nothing about your water though, and it could be the source of this problem. Well water is oftentimes very brackish and very high pH... and while it will work well in the ground, trapping it in a container can cause a problem.
There are still some unknowns here that make a proper diagnosis of this problem a little difficult, but let's attack the symptoms one by one and try to get this sorted. Tell me more about your water please, and how you determine that it is time to water, and how much water you add at each watering. Armed with those answers, we can get closer.