You don't need to use a "The world is doomed If they fail..." Plot point... Maybe the cultists are using the ritual to create a New cenobite, I mean chain outsider. Make the crystals, and the pain that brought them to the material, delimitate the abilities of the resulting new type of outsider, find some gruesome art on Pinterest, and done. Great adventure.
There are already "cenobites" in Pathfinder - they're called velstracs (or kytons in 1e). The original velstracs were formed from the first truly depraved thoughts of the early mortals. They horrified the gods so much that they chained them up in Hell, which they eventually escaped and now reside in the Shadow Plane. New velstracs are usually made by stealing masochistic/sadistic souls from the River of Souls and then torturing them until they transform. Their stated goal is nothing less than divinity, which they hope to achieve through enlightenment and physical perfection. That may sound all well and good until you realize that they seek the former by means of extreme suffering and the latter by finding creatures with body parts already superior to their own and then appropriating them. A velstrac that succeeds in this task and becomes a demigod is called a Demagogue.
I did know there were "cenobites", didn't know the name, or the lore... but taking your input of lore makes this even easier.
BBEG Velstrac wants to be a Demagogue and is experimenting on a way to directly harvest souls from the material, manipulating mortals and that sort of shenanigans. Motive for it? Insert reasoning for the suffering being more pure when it's still in their mortal husks so making more powerful minions and/or for harvesting parts, with the caveat of if the experiment fails the guys who were performing said rites dies, the guys would likely become harvesteable themselves so it's a win-win for the outsider really. For why the cult is doing that? Probably is a recruiting spree for those "artistic endeavors", so they would gather more guys for the cult and not simply dwindle their own loyal members numbers with these more risque approaches.
The "stones" could be a catalyst/result/subproduct of a failed/successful attempt of the ritual having strange effects, something like Agony/Liquid Pain had on 3.5 is a pretty good start.
I'm not sure there's really anything stopping the gods from just showing up on the material plane, apart from conventional rules of engagement and risks involved. If Desna could charged into the Abyss and brutalize a Demon Lord that one time, then I don't see why ZK couldn't make a trip to the material plane. But Desna's example also shows why gods getting involved personally tends to be a bad idea. And on top of that, you can ask Arazni what happens when you underestimate the dangers of the mortal world.
As for your question, I suppose that depends on how big of a danger do you want them to pose. Since your example suggests a threat to the entire globe, how about bringing a second Age of Darkness? With every other nation crippled, Nidal (which, thanks to their pact with the Midnight Lord, should be able to cope with eternal night fairly well) could then start conquering other lands with ease, eventually leading to a world-spanning empire dedicated to the worship of the Prince of Pain.
They're trying to create a stockpile of charged rocks for some obscure holiday in Nidal. The entire point is to make some Nidalese Noble's christmas party a real banger.
Pathfinder gods don't show up in person in the world.
Maybe something better would be related to the Star Towers - they could be doing it to enhance or repair one of them, adding a little spice in that stopping their sacrifices is a good act in the short term but might have consequences like a Spawn of Rovagug getting loose farther down the road.
Zon-Kuthon doesn't need a physical avatar. For the most part, most deities can hop on over to the material plane any time they want. What's holding them back is literally every other deity. Essentially, the deities are basically in a 100-way cold war with one another that would obliterate reality if it ever escalated. They don't want this to happen, and so they don't want to interfere too directly. Rovagug is the primary exception to this though.
Back to the Kuthites, I recommend looking into the [Black Triune](https://pathfinderwiki.com/wiki/Black_Triune) and considering them. A Zon-Kuthon cult would likely inevitably have ties back to Nidal and, as obscure as Nidal's leaders are, they would be the main motivators behind such a ritual. Because Zon-Kuthon is absolutely playing the long game, and the Triune would likely be involved in that. For example, ZK allowed Nidal to be dominated by Cheliex and subjugated into the empire, only for the Chelaxian empire to crumble and align itself with the forces of hell. Thus, giving ZK more power and influence in the world via Cheliax's new,growing, hellish influences. So wherever Cheliax's forces go now, Nidal's are somehow involved or working in the background. Thus, Zon-Kuthon is a deceptive guy who pulls many strings. And the Black Triune is likely to be a pivotal segment of the chain of events he's orchestrating
I also recommend giving the novel [Nightglass](https://pathfinderwiki.com/wiki/Nightglass) a read. It's a pretty quick read for a novel, I myself have just finished half of it casually over the past 5 days. It will give you insight into their culture, motivations, and interests in both Kuthite magic and religion.
If anything, such a ritual would have something to do with the Shadow Plane and the forces that exist there. Although, they do have a healthy respect (read: fear) of everything that exists on the plane. Either way, a Kuthite cult's interests would involve acquiring mastery, control, and 'liberation' from 'naive' concepts such as purity and morality. Ultimately, everything would become enslaved to Zon-Kuthon and his vision of the world.
Instead of Zon himself, perhaps its in an attempt to make contact with a velstrac or to become a velstrac themselves. Also, they likely would not be trying to kill the kidnapped people, as they wouldn't be able to feel pain in death, it would be more to their benefit to keep them alive but in pain.
They stones will be placed around a town or city, and then during the night of the ritual that whole area will be merged with the plane of shadows, allowing denizens of the plane to weak havoc on the population.
You don't need to use a "The world is doomed If they fail..." Plot point... Maybe the cultists are using the ritual to create a New cenobite, I mean chain outsider. Make the crystals, and the pain that brought them to the material, delimitate the abilities of the resulting new type of outsider, find some gruesome art on Pinterest, and done. Great adventure.
There are already "cenobites" in Pathfinder - they're called velstracs (or kytons in 1e). The original velstracs were formed from the first truly depraved thoughts of the early mortals. They horrified the gods so much that they chained them up in Hell, which they eventually escaped and now reside in the Shadow Plane. New velstracs are usually made by stealing masochistic/sadistic souls from the River of Souls and then torturing them until they transform. Their stated goal is nothing less than divinity, which they hope to achieve through enlightenment and physical perfection. That may sound all well and good until you realize that they seek the former by means of extreme suffering and the latter by finding creatures with body parts already superior to their own and then appropriating them. A velstrac that succeeds in this task and becomes a demigod is called a Demagogue.
I did know there were "cenobites", didn't know the name, or the lore... but taking your input of lore makes this even easier. BBEG Velstrac wants to be a Demagogue and is experimenting on a way to directly harvest souls from the material, manipulating mortals and that sort of shenanigans. Motive for it? Insert reasoning for the suffering being more pure when it's still in their mortal husks so making more powerful minions and/or for harvesting parts, with the caveat of if the experiment fails the guys who were performing said rites dies, the guys would likely become harvesteable themselves so it's a win-win for the outsider really. For why the cult is doing that? Probably is a recruiting spree for those "artistic endeavors", so they would gather more guys for the cult and not simply dwindle their own loyal members numbers with these more risque approaches. The "stones" could be a catalyst/result/subproduct of a failed/successful attempt of the ritual having strange effects, something like Agony/Liquid Pain had on 3.5 is a pretty good start.
I'm not sure there's really anything stopping the gods from just showing up on the material plane, apart from conventional rules of engagement and risks involved. If Desna could charged into the Abyss and brutalize a Demon Lord that one time, then I don't see why ZK couldn't make a trip to the material plane. But Desna's example also shows why gods getting involved personally tends to be a bad idea. And on top of that, you can ask Arazni what happens when you underestimate the dangers of the mortal world. As for your question, I suppose that depends on how big of a danger do you want them to pose. Since your example suggests a threat to the entire globe, how about bringing a second Age of Darkness? With every other nation crippled, Nidal (which, thanks to their pact with the Midnight Lord, should be able to cope with eternal night fairly well) could then start conquering other lands with ease, eventually leading to a world-spanning empire dedicated to the worship of the Prince of Pain.
Pain
They're trying to create a stockpile of charged rocks for some obscure holiday in Nidal. The entire point is to make some Nidalese Noble's christmas party a real banger.
Pathfinder gods don't show up in person in the world. Maybe something better would be related to the Star Towers - they could be doing it to enhance or repair one of them, adding a little spice in that stopping their sacrifices is a good act in the short term but might have consequences like a Spawn of Rovagug getting loose farther down the road.
Maybe the stones are building materials for a dark cathedral to Zon-Kuthon. They're building a temple to suffering, *out of* suffering.
By pain. With pain. For pain.
Zon-Kuthon doesn't need a physical avatar. For the most part, most deities can hop on over to the material plane any time they want. What's holding them back is literally every other deity. Essentially, the deities are basically in a 100-way cold war with one another that would obliterate reality if it ever escalated. They don't want this to happen, and so they don't want to interfere too directly. Rovagug is the primary exception to this though. Back to the Kuthites, I recommend looking into the [Black Triune](https://pathfinderwiki.com/wiki/Black_Triune) and considering them. A Zon-Kuthon cult would likely inevitably have ties back to Nidal and, as obscure as Nidal's leaders are, they would be the main motivators behind such a ritual. Because Zon-Kuthon is absolutely playing the long game, and the Triune would likely be involved in that. For example, ZK allowed Nidal to be dominated by Cheliex and subjugated into the empire, only for the Chelaxian empire to crumble and align itself with the forces of hell. Thus, giving ZK more power and influence in the world via Cheliax's new,growing, hellish influences. So wherever Cheliax's forces go now, Nidal's are somehow involved or working in the background. Thus, Zon-Kuthon is a deceptive guy who pulls many strings. And the Black Triune is likely to be a pivotal segment of the chain of events he's orchestrating I also recommend giving the novel [Nightglass](https://pathfinderwiki.com/wiki/Nightglass) a read. It's a pretty quick read for a novel, I myself have just finished half of it casually over the past 5 days. It will give you insight into their culture, motivations, and interests in both Kuthite magic and religion. If anything, such a ritual would have something to do with the Shadow Plane and the forces that exist there. Although, they do have a healthy respect (read: fear) of everything that exists on the plane. Either way, a Kuthite cult's interests would involve acquiring mastery, control, and 'liberation' from 'naive' concepts such as purity and morality. Ultimately, everything would become enslaved to Zon-Kuthon and his vision of the world.
Instead of Zon himself, perhaps its in an attempt to make contact with a velstrac or to become a velstrac themselves. Also, they likely would not be trying to kill the kidnapped people, as they wouldn't be able to feel pain in death, it would be more to their benefit to keep them alive but in pain.
They stones will be placed around a town or city, and then during the night of the ritual that whole area will be merged with the plane of shadows, allowing denizens of the plane to weak havoc on the population.