The airflow might be a bit much for those little seedlings, but it doesn't look like it's hurting them. I don't remember if you said what light you were using, wattage, led/incandescent, etc. If those pics are with the light on full, you probably still need more light.
There was someone here a while back growing in a similar situation who managed one plant per grow with a single 100W light and got pretty decent harvests. I can't remember who it was, though. I didn't see his thread in grow journals.
On the clear cups, I wouldn't cover them. Once you start seeing roots going down the side it will be time to up pot them anyway. If you're planning to leave them in 1 gallon pots to keep them small, you would do better moving them to fabric pots, purchased or home made, so they don't become root bound.
There was someone here a while back growing in a similar situation who managed one plant per grow with a single 100W light and got pretty decent harvests. I can't remember who it was, though. I didn't see his thread in grow journals.
On the clear cups, I wouldn't cover them. Once you start seeing roots going down the side it will be time to up pot them anyway. If you're planning to leave them in 1 gallon pots to keep them small, you would do better moving them to fabric pots, purchased or home made, so they don't become root bound.