DWC/LED grower here.
Personally if I use such setup as yours I would grow only from seed in order to avoid the problems that you have. This setup of yours is good for growing 2-4 plants (same strain because of the roots that would twist to each other) from seed to finish without transfering, it sucks for your purpose.
I see 3 bad things, first reality check- what is your led there-
http://www.compareledgrowlights.com/ I guess it is not powerful enough even at that early stage hence the strange stretching, and slow growth. The slow growth and stretching leads to the problems with the bacteria. The water level in your box should be just under the cup, you cannot down it in time because your plants develop roots slower then normal, and they do so because they have not enough light. You just need better light or to keep the light closer to the plants.
Second how you would transfer them if the roots twist into each other? Judging on your pic you have a week or so till this happens.
Third what you do to your water to keep it clean? There are 2 methods- either you sterilize it
with h202 or you grow beneficial bacteria that eats the bad bacteria. You can fully expect root rot and dead plants soon if you do nothing.
Also if you want to clone get/make cloner based on aeroponics. Try something like that- it is cheap and it works:
Notice at 2.01- your roots should be out of the rockwool before your put them into the water.
Also top feeding in DWG gets the hydroton full of algae and bacteria that slow down and damage your plants. When I do it from the seed I just wait 1 week at the tray till the seedling roots pops out of the rockwool than I keep the hydroton soked for only 1 week in the DWC (I cover the top on the cup with foil around the stem so no light can get into it to reduce algae/bacteria grow in the rockwool and hydroton), for 1 week the roots are as big as yours on the pic, then I change the hydroton with new one and lower the water level. All the time I use beneficial bacteria to prevent root problems.
