OK, I'll give these a go...and could be wrong...
Some things I didn't get from reading the rules:
1) What does it mean that Instant abilities and actions "take precedence over current abilities or actions"?
Does it mean that phase-specific abilities (actions) cannot be played on top of Instants? If so, can phase-specific abilities be played after the Instant resolves (say, on top of already played phase-specific abilities)?
Can another Instant be played on top of an Instant?
Instants 'trump' the preceding ability or action, for example, if a player chooses the "War" Fantos Action and then a player plays the Labour card "A Time of Peace" the "War" action is canceled.
There is no reason why you couldn't activate a Legacy's ability after an Instant was played, and an Instant can certainly be played after another Instant.
Do you have an example?
2) What does this mean (p. 18, "Fantos action phase", "Important notes"):
"If a Legacy or Citadel would like to collect any Fantos Action boosts from Labor Cards, those cards must be paid for before Tasking."
Doesn't this contradict the rule that Labor Cards may be played at any time before the final score for the Fantos action is established, in order to boost the score?
What I think this statement means is that since you have to pay for Labour Cards with UnTasked Legacies if you want to pay for a Labour card that gives you a Fantos Action boost using a Legacy that you are going to Task you need to pay for the card before Tasking that Legacy. AFAIK you can Task a Legacy to a Fantos Action and then use one of your UnTasked Legacies to pay for a Labour Card that boosts the Tasked Legacy.
3) If you can play a Labor Card that enhances a Fantos action before Tasking (per the note above), does that mean you can pay for the Labor Card using a Legacy and then task that same Legacy with the action?
4) When do the effects of abilities expire? In other words, when you play the Labor Card "Council": "Give a [Legacy] +3 [Tribute] for a single action.", do you have to do a Tribute action in that turn (or already be in the middle of a Tribute action) in order to benefit from the effect?
The card effect only lasts for that current action in the case of an Instant card. So in your example you would play "Council" either when you have chosen the Tribute Action or when another player has and you wish to put forward one of your own Legacies to attempt to become the Reigning Tribute.