The Naruto storyline was fairly coherent, but it was too "roundabout." It kept jumping back to the past and weaving the main plot through flashbacks to tell old stories. This also made the timeline unclear. On top of that, Kishimoto kept some characters' information under wraps. For example, almost everything online about Minato Namikaze was inferred from flashbacks, though those inferences were more or less certain. This made writing about events before the story began a real headache. Readers probably wouldn't scrutinize it too much anyway: they'd just accept whatever the author wrote, including that a character was born at a certain time. So here I'll lay out a fairly detailed timeline—one that's reasonably convincing.
First, for the Warring States period, the village-founding period, and the First Shinobi World War, you can read my other book, the Great Demon King. Those periods are explained pretty clearly there, and aside from the addition of a transmigrated protagonist, everything else is true. I also corrected a few obvious plot holes, like how the time Tsunade drank wine didn't match up with when Hashirama died. I won't go into more detail here.
Now for the main point.
First, we need to understand that the Naruto world is fictional, so it's bound to have plenty of plot holes. We can only do our best to fill them in, rather than overturn everything and make up our own version—unless something really can't be reconciled.
The Second Shinobi World War (Konoha Year–Year) lasted two years.
1. The countries involved: unlike the other two major wars (leaving aside the Fourth Shinobi World War), the Second Shinobi World War was fought mainly around one country, with Konohagakure, Iwagakure, and Sunagakure as the main parties. Which country was it? The Land of Rain, home to Hanzo of the Salamander, who was once known as a "demigod."
Here's the evidence:
1. The Land of Fire: There's a well-known story from the Second Shinobi World War: Jiraiya, Tsunade, and Orochimaru fought Hanzo of the Salamander and, though defeated, earned his respect and the title of "Sannin." Although the three of them lost despite fighting one man, Konohagakure won the war overall. Nagato's flashbacks also show that Konoha shinobi were sweeping through Amegakure, hunting enemy shinobi. Nagato's parents were mistaken for shinobi and killed. Amegakure was simply a victim of the great nations' war. Since Iwagakure of the Land of Earth and Sunagakure of the Land of Wind also took part in the war, their forces must have been there as well.
Note: When the war ended, Tsunade and Orochimaru both returned to Konohagakure, while Jiraiya stayed behind. You should remember why: Nagato, Yahiko, and Konan. The Sannin had come across the three wandering children by chance. Orochimaru suggested killing them outright so they wouldn't have to suffer through the war, but Jiraiya refused. After the war, Jiraiya stayed behind alone to teach the three for a while, then returned to Konohagakure. It was around then that Madara Uchiha transplanted his Rinnegan into Nagato. Based on the timeline, this should have happened between Konoha Year and Year 4.
The Land of Earth: Nagato's awakening should be memorable to everyone. So what actually happened? Not long after Jiraiya took in the three children, they were attacked by a shinobi. From the manga or anime, we can tell he was an Iwagakure shinobi. Nagato called him a "remnant of the shinobi," which makes it clear that the main Iwagakure forces had been defeated. Out of a desire for revenge, the survivors began harassing the Land of Rain, even attacking and killing its civilians for food.
The Land of Wind: After Chiyo was brought back with Impure World Reincarnation, she was revealed to be an old adversary of Hanzo's. She also knew the antidote to his poison and how long his summoning, Ibuse, took to produce venom. The conclusion is obvious: the Land of Wind took part in the war, and Chiyo had fought Hanzo of the Salamander.
Also, Sasori's parents were killed by the White Fang, and Tsunade countered all the poisons Chiyo prepared. These events happened around this time, which shows that all these people made a major impact in the war.
4. Aside from this main battlefield, the Land of Earth and the Land of Lightning also fought each other. From the flashback about the AB Brothers—the Fourth Raikage and the Eight-Tails Jinchuriki—we learn that the two of them fought against Iwagakure.
2. The timeline.
1. In Konoha Year 6, the beginning of Shippuden, Sasori was five years old. According to his profile, he graduated at seven, which means he graduated in Konoha Year 5. From Chiyo's flashback, we know that when his parents were killed, he hadn't yet learned ninjutsu. Chiyo later felt sorry for him and taught him the Puppet Technique to keep him occupied. In other words, his parents died before Sasori graduated, so they died before Year 5. Let's tentatively place their deaths in Konoha Year 4. The war must have started earlier, so the Second Shinobi World War began in Year 4 or before.
Nawaki died in the Second Shinobi World War. His ninja registration book shows that he died at age 1 and had the registration number 550. Another character, Mikoto Uchiha—the mother of Itachi and Sasuke—had the registration number 548, only slightly lower than Nawaki's. We can therefore conclude that they were basically in the same graduating class. As for their graduation age, because it was wartime and many shinobi graduated early, we can't tell whether they graduated in the same year. Now let's look at Mikoto's information: she died at age 5. In Konoha Year 60—the reason I keep using this year as a reference point should be obvious; it's when the story began—Itachi was 18. He wiped out his clan at age 1 (wasn't it 1?). In other words, the massacre happened five years earlier. If Mikoto had lived to Konoha Year 60, she would have been exactly 40, and Nawaki would have been around the same age. Nawaki died at age 1, which means he died 8 years earlier. 60 minus 8 is ... so he died in Konoha Year ... .
This narrows down the start of the Second Shinobi World War further: it must have begun in Konoha Year ... or earlier.
From Jiraiya's flashbacks, we know that Nagato had mastered all five chakra natures by the age of 10. In Konoha Year 6, when Shippuden began, Nagato died at age 41 (these ages at death were provided by Kishimoto). That means ... . He met Jiraiya 1 year earlier, in Konoha Year ... . The war had already ended by then. Jiraiya stayed in Amegakure to look after the three children, so the war fought in the Land of Rain must have ended in Konoha Year ... or at the end of Year 1. (It's possible Jiraiya met them right at the end of the year.)
We also know that Yahiko always came across as the big brother of the group, so we can infer that he was about the same age as Nagato, or perhaps older. Let's assume they were the same age. In the Pain's Assault arc, when Choji described the Deva Path's appearance, he said it looked to be about 5 years old. That means Yahiko died at age 5. (After his death, he was made into one of Pain's bodies, but his face of course stayed the same.) As discussed above, Nagato was 10 in Konoha Year ..., so Yahiko was also 10 that year. At age 5, that would put him in Konoha Year 47, right when the Kannabi Bridge battle in the Third Shinobi World War ended and Obito fell into darkness. After Yahiko died, Nagato accepted Obito's plan. Yes, it fits the story quite well.
4. Naruto talked with the Eight-Tails and wanted to know about his past. Then Motoi—the man who greeted Naruto when he arrived on the island—began to reminisce. Twenty years earlier, in Konoha Year ..., the Eight-Tails went berserk and Motoi's parents died. Motoi and Killer B, the Eight-Tails Jinchuriki at the time, were both five years old. That year was right in the middle of the Second Shinobi World War. From the flashback, we also learn that Killer B had already begun fighting on the battlefield alongside his big brother, the future Fourth Raikage. The AB Brothers gave the Iwagakure shinobi a terrible time.
5. From the manga, we know that Dan, Tsunade's lover, died during the Second Shinobi World War. Based on Dan Katō's age at death—7—we can also work out when he was born: Konoha Year 5 or 6. He was five years older than Tsunade. Given how much Tsunade admired Dan, that fits a young woman's feelings quite well. One detail doesn't make sense, though: Dan called Choza Akimichi "Big Brother Choza." There's nothing we can do but assume Kishimoto made a mistake; otherwise, there's no way to reconcile it.
So, as we worked out earlier, during the war between the Land of Fire and the Land of Wind in Konoha Year ... or earlier, the White Fang killed Sasori's parents. In other words, around Konoha Year ..., on the battlefield between the Land of Fire and the Land of Wind, the White Fang killed Sasori's parents, while Dan fell into Tsunade's arms.
That's basically all the information we have about the Second Shinobi World War, including the key figures and the major countries involved. We can see that most of the fighting took place between Konoha Year ... and Year ... . So we can conclude that the Second Shinobi World War began in Konoha Year ... and ended in Year ..., lasting two years.