I wait until the sprouts are about 5" across from leaf tip to leaf tip before I stat up-canning.
Sometimes bigger if they are a lanky strain.
You could always just cut the bottoms off of the cups when you have a few nodes on the seedling, and set the cups in a shallow hole in the 3-gal pots.
Zero stress transplanting.
I have a bad habit of leaving seedlings in the cups for too long sometimes.