When there is an event: Spend all of your AP on the event as it will be the most efficient use. Right now there is an event so do the event.

When there is no event: Do the 3 40 AP dailies once a day and do whatever you want with the rest of your AP (except for the lower AP dailies as those aren't worth the AP, a level 90 Support with class advantage + Jeanne for ember gathering can carry you through all the 40 AP nodes). The most efficient use of the rest of your AP as a new player are more 40 AP ember gather dailies.

The only reason to "focus on story mode" is if you need the saint quartz reward for the first clears asap because you want to summon some one. It doesn't make you any stronger.