2 week old seedlings' leaf damage

Let me start by saying this is my third grow. This is nirvana white widow fems at 2 weeks and 3 days from seed. No nutes, just PH water to ~5.7ph. The cubes are pretty low in the basket and i ran out of hydroton so the layer of hydroton stops right before the last row of holes at the top. I had the water level touching the bottom of the basket for the first two weeks then lowered it about an inch below the bottom 2 days ago. I have cardboard covering the top with a hole in the middle for the plant. The first sets of leaves look damaged on all the seedlings and on two of them, it looks like they're stained by water colors or something. The new growth so far looks ok. My questions are: did i keep the water level too high too long? is there not enough hydroton hence light getting in? the card board does a pretty good job of stopping the light, though. Should i use cfls instead of 600 watt hps when they sprout? but its over 3 feet above the babies and temps at the "canopy" are ~80F. should i trash them now and do something differently? are they permanently scarred and will eventually turn into thin, budless plants?

The 1st of your questions I can not answer other than never let the nutrient solution actually touch the medium in the pots. Only roots. 2nd the cardboard is doing fine. 3rd always use fluoros for the first two weeks of veg so it does not burn or stress your plant

thanks for the advice kblck. i will use it. am i good to go from here or should i start over?

keep it going, they will kick back up and do fine.