Well it's been over 12 hours and the plants look healthy.. Here is one thing I was thinking.

They say that if the roots get exposed to light it can cause the plant to go into shock. Well why not just transfer them when the second pair of leaves form. This way the roots are still covered in soil and no transplant shock.

My plants only had only a 1cm of root sticking out the bottom (not much root). I think by me transplanting these a little early they don't realize that they are in new pots. It almost seems to me that since the roots were within the original soil they din't feel anything.

this make any sense?