1. Some of the stone designs were changed after Factor Crafter when their effects were swapped around. It might be possible that the number also has connections to other physical properties of the stone (besides the effects coming from specific primes.)
2, 3: The stones are placed in cards, which, based on the notes in the lab, create copies of the stones and place them on the board. Because the copies have been "programmed" to have special effects (the card effects), I assume that the intense effects of the stones can be suppressed. You also can't just play loose stones, they have to be placed in cards.
4: The first player draws one fewer card at the start of their first turn.
5: I don't think so.
(This is just my speculation, it would be nice to have confirmation/correction from the developer.)