As with all roots, keep the taproot away from light. Should be fine letting them sit in the paper towel, though. I've had seeds with one inch long 'tails' that I had to cut-out of the paper to plant. Had no problems with them at all, but that was really pushing it, I think. (I ran out of soil for a week)

I've never used rockwool, but isn't 5.5 ph water, combined with using the (acidic) rockwool, a bit too acidic to start seeds...? I have heard of others' rinsing and squeezing the cubes, to alleviate this, (like rinsing out a sponge, rinse, squeeze, rinse, squeeze...) but don't know firsthand.