I uploaded an update of rulebook (beta version).
Expansion: ... If a Civilization expands into an empty territory, it
gains the Territory Bonus of the Territory Token.
Just my personal taste here, but I like "... it gains the VP specified on the Territory Token." It seems strange to call it a Territory Bonus when it's never anything other than VP. In fact, "Territory Bonus" is only used twice in the rule book in a different meaning each time (the first being here where it is the amount of points gained upon expanding, the second being the act of gaining points at the end of a Turn).
Also, stick to "gains" VP or "scores" VP. You use both interchangeably.
Raid: ... Note that a
Civilization in the same territory as you is
considered adjacent, and may be raided.
If the same is true for the Trade action as well, it should be noted there. You may also want to note the raided player doesn't lose anything, as that is unconventional (both in real life, and in civilization board games).
If a player's last cube in a territory is removed, do they lose VP as if they removed it themselves via the Exploit action?
Turn Example ... Ada uses 1 Power cube and
gains 1 technology level.
Bea uses 1 Power cube and
gains 1 military level. She then
moves one cube from the Used
cube pool back in front of her
(The bonus associated with
attaining level 2 military).
You note the military bonus, but you don't note the technology bonus ("Ada adds the War action card to her hand").
You might want to specify that the turn marker is advanced after a turn ends, that the Age marker advances after the 4th turn of each Age, and that the game ends if this is the 4th turn of the 3rd Age. It can be assumed, of course, but I found it strange that it was never mentioned (and who knows, one of your players may get confused).
Recover 1 Power Cube and Gain 2 VP
Nothing wrong here, I just wanted to say how cool and thematic this is.
Wonder Cards: A player can activate as many wonder cards as he
wants during his actions.
Under a literal reading, a player may activate a wonder even in the middle of performing another action (such as after recovering a cube but before expanding with the Advanced Expand action). Actually, when read literally, that is the only time you are allowed to activate wonders. Also, I'm not sure if advisors count as actions.
I'm guessing this isn't intentional, so I'd put "A player can activate as many wonder cards as he wants before or after resolving one of his action or advisor cards."
And in this section, you call the points gained when expanding an Exploration Bonus, when earlier it is called the Territory Bonus. I think both terms are unnecessary, but at least stick to one. I'd say the whole section following "Territory tokens also have a unique number on them. This is the territory number (used with Civbots)" is unnecessary as this information has already been given multiple times in the rulebook (even in the preceding paragraph!)
Didn't read the section, just make sure to keep wording consistent.