At present, the system of Honor and Glory presently leaves a lot to be desired for. Linking the "Virtue Advantages" and "Virtue Disadvantages" to particular Bushido virtues is interesting, but not necessarily what I feel is the proper course of action. I feel there needs to be more direct interaction between Ninjo and Giri and the Honor mechanics / Bushido virtues.

The simplest way to do this is to work how the Ninjo and Giri systems work. At present, as best as I can tell, this is how they work:

• When given an opportunity to fulfill their Ninjo, the character can indulge or deny. If the character denies their Ninjo, they gain Strife equal to their honor rank (which is itself an awkward nomenclature, because why is honor on a scale of 0 to 100, and yet still has ranks?) and potentially lose some honor.
• If the character manages to overcome their Ninjo, they gain some honor. If they satisfy it fully, they lose some honor. In either case, they then choose a new Ninjo.
• When given an opportunity to fulfill their Giri, the character can commit or refrain. If they refrain from fulfilling their Giri, they gain Strife equal to their glory rank (see above), and possibly lose some glory as well.
• If the character manages to completely fail their Giri, they lose some glory. If they resolve it fully, they gain some glory.

This system is, honestly, weak. For one, it is a punishment system, rather than a reward system. Players will (usually) prefer reward systems than punishment systems. This encourages the metagame to AVOID the drama at the core of the story, because mechanically, there is no reward. For another, this system only connects to the Strife system and the Honor / Glory system. This separates it far too much, mechanically, from the rest of the game. The dramatic conflict between Ninjo and Giri is at the HEART of samurai drama, and it should be the fire burning bright in the heart of the games engines. The mechanics of the game should help tell the story of the conflict between Ninjo and Giri at every opportunity. Just as the Fate Economy of the LCG enforces the theme of mono no aware mechanically, Ninjo vs Giri should be expressed to a much greater extent.

My proposed change is this:

1. Set Honor and Glory aside for the moment. There is a lot in this system which needs to be overhauled as is, and it should be more integrated into the game. For the moment, set it aside.
2. When choosing a Ninjo for their character, the player must also choose a Bushido Virtue for that Ninjo. It is in the failure of this Virtue that this Ninjo is expressed. For example, the Ninjo "Stay Alive" can be a Failure of Courage, "Be with the one I truly love" can be a Failure of Duty, "Discover my true parentage" can be a Failure of Sincerity, "Take revenge on the person who murdered my father" is a Failure of Compassion, and so forth. This frames the Ninjo chosen by the player in terms of how that "human desire" is a betrayal of the code of Bushido. It makes even the most virtuous of samurai have something about them which is a Flaw.
3. When choosing a Giri for their character, the player must also choose a Bushido Virtue for that Giri. It is the particular Virtue that this "sworn duty" best represents. "Doing whatever my Lord tells me, no matter what" is an expression of Duty, "Persuade a powerful leader to ally with my Lord" is an expression of Sincerity, "Deliver criminals to justice" is an expression of Righteousness.
4. Once per session, when a character is confronted with the option to indulge their Ninjo, they must choose to either Indulge or Deny. If they Indulge in their Ninjo, they may remove Strife and Fatigue until they are below half of their Composure and half their Endurance, respectively. If they Deny their Ninjo, however, they gain 1 Void Point as they affirm their own control over themselves and their devotion to Bushido.
5. Once per session, when a character is confronted with the option to fulfill their Giri, they must choose to either Commit or Refrain. If the character Commits to their Giri, they may remove Strife and Fatigue until they are below half of their Composure and half their Endurance, respectively. If they Refrain from their Giri, they gain 1 Void Point as they affirm their own control over themselves at the cost of Bushido.
6. Optional: The character gains the Paragon of Bushido for the tenet that matches their Giri, and Failure of Bushido (better name than Disdain for a Bushido Tenet) for the tenet that matches their Ninjo.

I feel this system makes the choice of Ninjo and Giri more mechanically interesting, as it builds in an effective "refresh" for either fulfilling the Giri or indulging the Ninjo, but also gives a method of gaining a Void Point by choosing to either be selfless (Ninjo) or selfish (Giri).

I definitely agree that Giri-Ninjo isn't done quite right in the game. I have though about simply attaching it to a Bushido virtue for both of them as well, and as I think on it I keep coming back to the same thing. Have a player pick a virtue to be their Giri - this is the virtue they believe in. Pick another to be the Ninjo - this is the virtue that they take exception to.

When it comes to rewards and penalties I just don't like the honor / glory track. I'd honestly be just as fine taking that away entirely, allowing the players and GM to rp what they want, and allow the GM to design what interactions come from being honorable or dishonorable in the story. Honestly its just more paper work to me.

This is why I think tying it to Strife and Void makes it more central to the game mechanics, rather than tying it to the Honor & Glory system, which does not interact with the rest of the game nearly enough. Adding the Distinction and Adversity to the mechanics as well also helps with that.

Have a Giri which helps you be more Courageous? Reroll those dice! Have a Ninjo which makes it hard for you to be Righteous? Reroll those successes.