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If I remember correctly, Ebullience is calculated after everything else.

Taken from: http://wiki.ffxiclopedia.org/wiki/Ebullience

* Ebullience is a stratagem, which obeys different usage rules than typical Job Abilities.

* Increases potency by 20%. Works with drain, aspir, bio, nukes, and helix. Does not work with enfeebles.

* The potency increase is calculated after all other factors, including Magic Attack Bonus and day/weather bonuses.

You see why this matters more at high levels, right? Testing Stone isn't going to really let that JA shine.