The Ninja specializes in evasive techniques, so you want to take advantage of that. Utsusemi and Shunshin will see most attacks miss your character (try guiding physical attacks toward yourself with Kairai or Provoke if the enemy seems to prefer attacking your other characters), but that alone won't help your damage output. What you can do, though, is couple them with passive abilities that bolster your abilities when you dodge attacks.
For instance, use Turn Tables and Redoubled Effort together, and once you dodge a couple attacks, you should gain a few extra BP and experience a very nice damage boost until you fritter it away. Using Ikkikasei might also help you make the most of Frenetic Fighting, although you'd be giving up a couple BP to attack on the same turn. In this case, you might prefer Comeback Kid in place of Redoubled Effort to take advantage of the steady attack buffs instead.
If you're using Sword Magic as your secondary skill set, I'd recommend having someone with the Salve-Maker's Medication command backing them up. Bring lots of elemental ingredients and Insect Antennae to make element-weakening compounds to max out the effects of those blade enchantments. Don't be afraid to use the high-level enchantments, either, as they last a whopping ten (count 'em, 10) rounds of combat! Plus, your Spell Fencer job level gives you the option of an Aspir enchantment to replenish your MP if you start to run out. If it were me, I'd prefer to sacrifice damage output for a few turns by regaining MP, not just for lack of it.