There are a couple approaches.

First option - don't. Make real sure your group is on board with this, because many people find scenes like that at the table unacceptable (and it's not just binary, there's also the depth to which you go into it). There's a lot of related topics (loss of control, permanent effects on a character, squeamishness, other psych issues) that really bother people about it.

I and my gaming group aren't really squeamish, so we'd skip past that option, but it's worth saying.

Second option - make it a mechanic. Some games specifically have skills for that - in Alternity, there's both Physical Resolve and Mental Resolve stats that can be used in a simple or complex skill check situation to quickly simulate torture and the PC "giving it up" or successfully holding out/giving false information. In D&D you might use opposed Concentration vs Intimidate/Profession:Torturer, Bluff vs. Sense Motive, or similar. In L5R, there is actually a Low Skill called "Torture," I would assume you'd use that.

The use of Torture is dishonorable because it involves touching blood, sweat and dead flesh. When using Torture, a character is trying to extract information from the tortured character using pain. Torture is a contested Awareness+Torture roll vs. the opponent's Stamina (deducting a number of dice equal to his current Wound level, of course).

The main drawback here is that players always hate control being taken away. Sure, there's always charm and paralyze and stuff, but it is often even more objectionable when there's not the excuse of "it's magic and you failed your save."

Third option - make the PC feel it. Have the torture do not just "hit point" damage - do stat damage, some temporary some permanent (or whatever analogue of that L5R supports - reduce Traits, for example, or apply Disadvantages like "totally jacked up"). See if permanent damage convinces them to talk. The main drawback here is that many players will just opt to die rather than talk, as it's an easy choice to make, and if left with a crippled PC they'll just demand to roll a new character/commit suicide/leave the group and call you names.

You can't

It is not possible for you to model the thought processes of God, no matter how much time you spend on it. There are too many fundamental barriers to emulating its mind, some of which you have touched upon in this question and in your previous one.

The silver lining here is that your players aren't in a position to do this either. Nobody, in the game universe or at your game table, is qualified to do this. So don't do it.

Don't play God as a character

God is a singular, primeval force. It will do what it does, and there isn't any reasonable way to explain, categorize, or justify any of those things in any true way. But that's fine. Humanity has been attempting to explain, categorize, and justify the actions of God for thousands of years, and the impossibility of it has never really stopped us.

God is a story. It's a story that you're going to tell your players, because that's the story that their characters are going to invent to justify the experience they just had. Something happened to them that fundamentally cannot be explained, and so they will paint over it and fill in the rough edges and do whatever they have to so that they don't all go insane.

There is never just one story

This encounter with God is not an objective event. It can't be. Every single one of the characters is going to fit their own story to what happens. Every single one of the characters is going to think they figured it all out. And they're all wrong. But they're all right.

You need a way to tell this story in multiple ways to multiple people at the same time. It's not going to be easy (I hope you didn't expect it to be).

1. Come up with a metaphor of God for each of the characters. This shouldn't be elaborate, but it's a lens through which you can craft the characters' unique experiences. Think about the varying manifestations of God in our world. These are all different people attempting to explain the unknowable. This metaphor will also probably suggest some human-like personality qualities of God; use them to further differentiate responses.
2. Come up with the intended outcome of the scene. This is where God is going to be steering the whole experience, and knowing about this goal will make it easier to improvise the events of the scene. You're going to be improvising a lot. This goal allows you to craft the story of this scene, which is really all there is to it. The rest is just expression.
3. Sit everybody down at the table. (If you're playing in some non-real-time format, this is significantly easier, but it doesn't sound like this is the case.)
4. Announce and enforce a very strict no-meta-talk rule during this scene. Everything your players say about the game must be in universe. If they want to coordinate perceptions, they're doing it explicitly.
5. Pass each of your players a card telling them what their character perceives at the start of the scene. This should map to each of their metaphors, but all of the descriptions should have similar themes (keep in mind the scene goal).
6. Let the players describe their characters' actions, and then write out how God responds to each of them. The response should be based on whatever any of the characters has just done, but each will see a different reaction. This is going to be slow, because you have to think about the responses and then write several of them, but that's pretty unavoidable. Remember that you are in some sense portraying a different scene to each player, but that the end goal is the same for all of them. This can get very slow, so simplify the communication as much as possible on your side: speak with brief, vague statements; use imagery rather than words; and don't be afraid of your signals being too subtle. All of these things contribute to the ambiguity of the encounter, which is exactly right.
7. Eventually, the scene reaches its goal, God leaves, and everyone can go back to however you normally play. Depending on how much you tailor to each character, their recollections of the scene could be very different, which is a good thing.

At the end of this, the characters have each experienced something very different, but the fact that all of their actions were interwoven consistently and that there was that single secret goal that you were working from should provide enough similarity for them to agree that something happened to all of them and that there's a direction to go next.