Sounds like your problem is not taking any risks.
Your too worried about keeping your own guys. You should be attacking him at every turn. Regardless of if you can actually take the province. Ninja decks pack a 2-1 Pk Ratio. Even just going into battle and scrapping it out puts tempo in your favor. Never let the build up continue. Also, Ninja decks are fantastic at retreating and movement. So go into battle, kill some guys, lose one of yours, then go home.
You should never let the game get to the point that you did. That has less to do with deck design and more to do with bad playstyle. (sorry for being honest here) but that really is a bad call.
Look at it this way. Ninja decks play an attrition match... if your hesitant to both attack and defend because your afriad, remember this: Most people only pack a few pk actions in their deck. Hired Killer, Ruthless Advance, Flanking Action, and Peasent Vengence. You know if your are playing a dueler off the bat.
Ninjas get: KW, Vengeful Shadows, Parley, Silent Movements, Ruthless Advance, Hired Killer, Goju Zeshin, Bayushi Arashii, Bayushi Yumita, Unseen Asailent, Furious Assualt + Tsimaru Combo, Flanking Action, Crude Trap....
If your battle actions don't go like this:
Kill a guy.
Kill a guy.
Kill a guy.
Move a guy. React. Kill a guy.
Go home. Kill a guy.
Bow a guy. Kill a guy.
Then your ninja deck needs to be re-worked from the ground up. Just scrap it and start over from scratch.
Much of the social history of the western world has been replacing what worked with what sounded good.
