1. Remember at the end of last season Dolores left the park in Charlotte's body, but then switched back to her own. So somebody else is inside Charlotte's body now - we have no clue who yet! We know that one of the mystery mind-marbles was Bernard, but the rest are still unknown. Some people think that Dolores is likely to have taken the pearls of her host comrades - Angela, etc - to take control of those bodies, but i'm of the opinion that she could have downloaded the human minds from the Forge and 'tweaked' them to match her needs (similar to what she did with Bernard). We learn that Conells also visited Westworld which supports this a little bit, as his mind would have been within the Forge.
As of now, there's still two mystery pearls from the bag 'o balls.
2. Yep, Tommy's character was a human before.