3 – If I’m playing a 2 player game and one player is eliminated: 1. Will the villain activate an additional…

No and no; during the villain phase, the villain will only activate once against each remaining player, and only one encounter card will be dealt to the remaining player.

I’ll add that any “Per Player” icons will calculate their values based on the number of players that started the game, but beyond that, everything you need to know is covered in the “Player Elimination” rules.