Ninjutsu rotation should be something like this:

Is Huton up? if not, use Huton
Is Trick Attack ready? If yes, Use Suiton > Trick attack
If Huton is up and Trick attack on CD, use Raiton

In the case of Kattsassu being available, you will want to use it as immediately as possible after a ninjutsu, regardless of what that was. During my burst rotation at the start of all fights my ninjutsu goes exactly like this.

Prepare by using Huton pre-fight.
Use Suiton > Katsassu > Trick Attack > Raiton, weaving between your rotation as much as possible.

This accomplishes two things.

Your strongest attacks are used early while all buffs and potions are rolling if u use them.
Your Trick Attack is buffing the raid during their burst rotations at the start of the fight.


Beyond this rotation, you only have to keep up your dots, and if nothing else is avalable, use your filler rotation (Aeolian Edge).
Your Warrior will likely keep Storm's Eye up for you. If not, you may want to keep it up yourself (I'm not sure if it is actually a DPS increase to do so.).

Oh, and as for Doton (that ground AoE), I'm fairly certain it is not an increase in DPS on a single target. Maybe on two targets it is.
Also, Raiton and Katon are fairly equal in damage when against 2 targets, so as soon as you see three targets, use Katon instead of Raiton. Katsassu will guarantee a crit on all targets hit with Katon.