First you shoudl decide if you are writing a Character story or an Idea story.
A Character story is about the personality and development of a person. Its about their growth (or degeneration) and how it effects their lives and the lives of those around them. It starts at the moment when the main character chooses to change their world, and ends when that character either succeeds or fails.
An Idea story is about the expolration of a idea or question. It focuses on exploring the details of this question and how the implications of the possible answers effect the world. It starts when the main character first encounter the question and ends when the question is answered.
The reason you want to decide which this is is because that will tell you how to treat the story. If the story is about Character then the main character must undergo a process of personal discovery and exploration, with lesser amounts devoted to other characters. The important part is that this change and evolution is mandatory in a Character story.
If the story is about the Idea then exploring the Idea is the important part. In such a case, you choose which characters represent which potential "answers" to your central question. Then you craft their character based around that and use them in that roll. The important thing is that in this case, change is not mandatory.
The reason I'm bringing this up? Because your story is NOT a milieu story. The setting of your story really isn't important to the telling of your tale. Its a stage on which your characters get to talk to each other. Thus, you don't have to sweat the details too much. If your story is a Character story people will accept it so long as you pay token attention to details and don't violate the "rules" of your setting. If your story is an Idea story then the setting elements can be used allegorically to represent the core concepts of the question and its various permutations and once again the readers won't mind.
So, unless you plan on turning this into a milieu story (ie, the roadtrip is what's important) don't sweat the small details of the setting. Paint in braodstrokes and don't go into too much detail except where it creates emphasis either on the thoughts and actions of the characters or the way they express the central idea.
For instance you mention Gideon not giving much thought to "how the sewers run". Well, perhaps you can explore that idea if you think it will emphasize the Idea of the story. If your central tenant is that "godlike power is bad" than point out how Gideon's selfish actions have led to blocked sewer pipes, growing disease, starvation (due to lack of irrigation), pollution and other factors that are (just now) beginining to adversely effect the world. This will emphasisze in the readers mind how selfish and childish Gideon's understanding of the world is. If you want power to be seen more as a blessing, then have the sewers and such work... despite how poorly thought out they are. Things like overflowing and backwash and disease and water reclamation aren't problems because Gideon doens't WANT them to be problems, so they aren't. This will emphasize to the readers that despite his claims to the contrary this world NEEDS gods because without them it will break down.
Constantly look at each part of your world with an eye towards how this part will emphasize the story you want to tell. A powerful set piece can very easily tell more about the characters and the idea then a poorly chosen one would. Do NOT fall into the trap of including setting pieces "just because". Every location in this roadtrip should be chosen to emphasize what is happening with the group. If nothing interesting happens at a location, cut it.
That being said, here is some general advice:
Establish how magic works and establish this in your story EARLY. Make the rules, then never break them. You have a grace period, about 20-30 pages in which the reader is willing to let anything go. After that, unexplained surprises and asspulls will do nothing but annoy them. This means that you have to introduce the concept of Gideon's divinity EARLY and establish what his limits are just as early. You can leave in the air whether these limits are externally or interanally imposed, if you want. But at this stage you are forming a contract with the readers and if you violate it they will be (rightly) pissed off at you.
Since religon is such a major part of your story you should put a LOT of thought into it. Does this world still have god worship? In what forms? Is their atheism? Monotheism? Does the Godslayer have a cult, or even a fully organized religon? How do the normal people view religon? Is it seen as immoral to be areligious? Is it seen as immoral to be religious? Even people in the modern world have lots of strange superstitions, so the people in this world are bound to have lots more (worse yet, many of these worked up until X years ago).
How do the normal people view the reality shift? Are they, by and large, happier? Do they understand how eveyrthing works or are they just stumbling through the motions. Modern medicine is a great boon, but if the "doctors" only know that if you stick a persona with symptoms A and B with Needle C to make them feel better and have no deeper understanding of disease and biology then the system will fall apart rather fast. Similarly electric lights are great, but if people don't understand the physics involved they'll be lost. Maintaining power plants will become ritual, not understood. It will take on religious implications (see above). On the other hand, if Gideon downloaded a complete understanding of modern science (as far as he understands it!) into the brians of all the scholars and enginneers then things will be much easier. People will innovate and explore in ways that Gideon never imagined, because people are like that. They may even start innovating in ways he doesn't LIKE.
Magic is the other magic leg of your setting tripod. You have to decide how it works. What can magic accomplish? How much does it cost? Is it inherent, learned or mystical? How does it interact with technology? How COMMON is it? If ever Tom, Dick and Haragon has magic, it loses some of its wonder. If its limited to wizards and preists, it becomes arcane. If its VERY rare, it becomes mythic. How do "normal" people view magic? Distrust? Worship? Despair? Is magic an amoral force, or does it have higher moral underpinnings? Even if it has none, this is a VERY important question since it changes the answer to the question and the way the characters grow.
Consider magic carefully. A magic that is more symbolic might help emphasis Ideas in your story more, while one that is more freeform will express itself more in the personality of the Character who wields it. Think of magic as another part of the setting. Each piece of magic should serve to emphasize a part of either the characters development or the question.
What this boils down to is that the answer to your question here shouldn't be hard and fats laws. The answer is always "what makes for a better story here?". As long as you don't violate your own continuity, the type of story you are telling allows you to get away with a LOT of handwaving of small details.
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Epsilon
A Character story is about the personality and development of a person. Its about their growth (or degeneration) and how it effects their lives and the lives of those around them. It starts at the moment when the main character chooses to change their world, and ends when that character either succeeds or fails.
An Idea story is about the expolration of a idea or question. It focuses on exploring the details of this question and how the implications of the possible answers effect the world. It starts when the main character first encounter the question and ends when the question is answered.
The reason you want to decide which this is is because that will tell you how to treat the story. If the story is about Character then the main character must undergo a process of personal discovery and exploration, with lesser amounts devoted to other characters. The important part is that this change and evolution is mandatory in a Character story.
If the story is about the Idea then exploring the Idea is the important part. In such a case, you choose which characters represent which potential "answers" to your central question. Then you craft their character based around that and use them in that roll. The important thing is that in this case, change is not mandatory.
The reason I'm bringing this up? Because your story is NOT a milieu story. The setting of your story really isn't important to the telling of your tale. Its a stage on which your characters get to talk to each other. Thus, you don't have to sweat the details too much. If your story is a Character story people will accept it so long as you pay token attention to details and don't violate the "rules" of your setting. If your story is an Idea story then the setting elements can be used allegorically to represent the core concepts of the question and its various permutations and once again the readers won't mind.
So, unless you plan on turning this into a milieu story (ie, the roadtrip is what's important) don't sweat the small details of the setting. Paint in braodstrokes and don't go into too much detail except where it creates emphasis either on the thoughts and actions of the characters or the way they express the central idea.
For instance you mention Gideon not giving much thought to "how the sewers run". Well, perhaps you can explore that idea if you think it will emphasize the Idea of the story. If your central tenant is that "godlike power is bad" than point out how Gideon's selfish actions have led to blocked sewer pipes, growing disease, starvation (due to lack of irrigation), pollution and other factors that are (just now) beginining to adversely effect the world. This will emphasisze in the readers mind how selfish and childish Gideon's understanding of the world is. If you want power to be seen more as a blessing, then have the sewers and such work... despite how poorly thought out they are. Things like overflowing and backwash and disease and water reclamation aren't problems because Gideon doens't WANT them to be problems, so they aren't. This will emphasize to the readers that despite his claims to the contrary this world NEEDS gods because without them it will break down.
Constantly look at each part of your world with an eye towards how this part will emphasize the story you want to tell. A powerful set piece can very easily tell more about the characters and the idea then a poorly chosen one would. Do NOT fall into the trap of including setting pieces "just because". Every location in this roadtrip should be chosen to emphasize what is happening with the group. If nothing interesting happens at a location, cut it.
That being said, here is some general advice:
Establish how magic works and establish this in your story EARLY. Make the rules, then never break them. You have a grace period, about 20-30 pages in which the reader is willing to let anything go. After that, unexplained surprises and asspulls will do nothing but annoy them. This means that you have to introduce the concept of Gideon's divinity EARLY and establish what his limits are just as early. You can leave in the air whether these limits are externally or interanally imposed, if you want. But at this stage you are forming a contract with the readers and if you violate it they will be (rightly) pissed off at you.
Since religon is such a major part of your story you should put a LOT of thought into it. Does this world still have god worship? In what forms? Is their atheism? Monotheism? Does the Godslayer have a cult, or even a fully organized religon? How do the normal people view religon? Is it seen as immoral to be areligious? Is it seen as immoral to be religious? Even people in the modern world have lots of strange superstitions, so the people in this world are bound to have lots more (worse yet, many of these worked up until X years ago).
How do the normal people view the reality shift? Are they, by and large, happier? Do they understand how eveyrthing works or are they just stumbling through the motions. Modern medicine is a great boon, but if the "doctors" only know that if you stick a persona with symptoms A and B with Needle C to make them feel better and have no deeper understanding of disease and biology then the system will fall apart rather fast. Similarly electric lights are great, but if people don't understand the physics involved they'll be lost. Maintaining power plants will become ritual, not understood. It will take on religious implications (see above). On the other hand, if Gideon downloaded a complete understanding of modern science (as far as he understands it!) into the brians of all the scholars and enginneers then things will be much easier. People will innovate and explore in ways that Gideon never imagined, because people are like that. They may even start innovating in ways he doesn't LIKE.
Magic is the other magic leg of your setting tripod. You have to decide how it works. What can magic accomplish? How much does it cost? Is it inherent, learned or mystical? How does it interact with technology? How COMMON is it? If ever Tom, Dick and Haragon has magic, it loses some of its wonder. If its limited to wizards and preists, it becomes arcane. If its VERY rare, it becomes mythic. How do "normal" people view magic? Distrust? Worship? Despair? Is magic an amoral force, or does it have higher moral underpinnings? Even if it has none, this is a VERY important question since it changes the answer to the question and the way the characters grow.
Consider magic carefully. A magic that is more symbolic might help emphasis Ideas in your story more, while one that is more freeform will express itself more in the personality of the Character who wields it. Think of magic as another part of the setting. Each piece of magic should serve to emphasize a part of either the characters development or the question.
What this boils down to is that the answer to your question here shouldn't be hard and fats laws. The answer is always "what makes for a better story here?". As long as you don't violate your own continuity, the type of story you are telling allows you to get away with a LOT of handwaving of small details.
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Epsilon