The one on the left, first picture, throw it away. The second one can be salvaged....don't immediately transplant. You just should not have used that cup. Wrap a piece of white paper around that clear cup. Once roots have developed, they will not appreciate light exposure. Since you love checking in on your roots...just unwrap the paper to check.
Secondly, roots NEED oxygen to develop properly. To salvage that second one.....poke at least 100 holes (with sterilized safety pin) around entire cup....no shit. Think of your clone as a sponge that you don't want to oversaturate, but only keep lightly moist. You need to mist 2-3 times a day. LOL, I know you want specifics......say 14-21 shots all around the perimeter AT LEAST twice a day (yet no more than 3)......no more dome necessary.
Now, do NOT plant the rest of your clones in those cups. Go with something slightly larger, bearing in mind that you need not transplant more than one more time. Fish emulsion---e.g. Neptune's Harvest, is more than adequate for nutrients right now. Do NOT use anything stronger at this point.