Why aren't you at your post?
Q1: Do the 12 'replace' the normal villain group and henchmen you would use, or are they 'in addition' to?
In an Advanced Solo game, the SHIELD Officers are in addition to the singular Villain Group for this Scheme.
Q2: But do I play another card from the Villain deck this turn? It only says on Twists 1 through 6 to play another card from the Villain deck.
You do not play another card from the Villain Deck on the seventh Twist. If playing Advanced Solo, you do however put a hero that costs 6 or less on the bottom of the Hero deck.
However, at this point, there aren't enough SHIELD Officers left (3) out of the 4 remaining cards (so they can't advance 5 city spots anyway), and there are no more Twists, so Evil can't win. I also read this that I would run out of cards in the deck and these 3 would not escape, thus a 'draw'. Anyone see an issue with this?
This would be as intended. In this case, Evil cannot win.