The boons you roll to score a crit on your boons, does it "use up" the boons or can you still use the boons to trigger action card abilities or recover fatigue/stress? Or do you have to choose to apply the boons to your attack roll to score that crit? Assume you don't get multiple crits if you roll a lots of boons, and only ever one outside of bonus crits from action cards.

It "use up" them. I'm not sure I understand you last question, but if you have multiple boons, you could activate multiple different boon effects. For example, you get 7 boons(!!), you could use 3 to activate your weapon critical, use 2 to activate the +1 critical from your action card and use the remaining 2 to recover one fatigue from universal effect.

EDIT : If any doubts, I've found the official rule on p.45 Rulebook.

Effect Triggering Limits

Each individual effect can only be triggered once during any single
task.

[...]

Even though a single effect can only be triggered once per task, it is
possible (if enough banes or boons are generated by the dice pool)
to fuel several different effects in the same task.