Thanks for playing! Card sized rules & player aid are a good idea. I'll give that a look once I have some time to revisit this.
To answer your rules questions:
Valley Guardian: Connected just means spaces that touch each other in a group. For the purposes of Valley Guardian, only mountains separate the groups.
Close Neighbors: This scores in square number increments (so, 1/4/9/16/25). You're right that it's probably not worth it if your biggest square is only 3x3, but a 5x5 can be very juicy.
Land of Plenty: You do lose 10 points for this one, yes.