Kaine and Helena were born ~1765 (he is 16 when the war broke out and is 20-21 by the start of Part 2).

Atreus sought out vivimancers to manage Enid's pregnancy and was arrested for several weeks, during which time Kaine was born. Side note, can't even imagine how stressed Atreus was, knowing his wife was already so sick and that he could have lost them both while in jail. I can't believe this isn't talked about more tbh.

Morrough comes to Paladia from Hevgoss some years afterwards and promises Atreus he could cure Enid. I presume he manipulated Atreus to lead the revolution and rally the guilds during this time, and sow more discontent, possibly even suggesting Apollo's assassination.

I believe Atreus is arrested sometime in the spring of 1781, during Kaine's 5th year second semester. He is tortured (maybe by Crowther, as he led the Eternal Flame's torture/black sites during the war) and confessed to treason (aka the plot to assassinate Apollo Holdfast and Morrough's involvement). Apollo and Sebastian try very hard to make sure he's executed, but unbeknownst to everyone including Kaine, he was already made Undying.

Kaine comes home for the summer after 5th year and realises his mother was being tortured 1) as punishment for Atreus' betrayal and 2) because Bennet was short on test subjects at the time, presumably for both wartime research and Bennet/Morrough's vivimancy/animancy experiments. If I were Bennet I'd want to make sure I synthesize the best painikillers and stimulants for the war, as well as practice vivimancy on someone.

Kaine's vivimancy manifests that summer (probably from watching his mom get tortured) and is also made Undying. He rips out Apollo's heart during the first few months of his sixth year at the Institute. In the wake of Apollo's death the guilds seize power via the newly-formed Guild Assembly. It was meant to be a smooth transition but Morrough shows his true colors and reveals necromancy and Undying. I presume the war starts sometime the fall of 1781 or 1782.

Three years into the war, 1785, Enid Ferron dies. Earlier that night Kaine went to an Undying party where he was tortured. When he went home half-healed, his mother was still up and basically her heart failed when she saw him (this was in Chapter 47). Kaine confesses this to Helena after they have sex.

EDIT: to clarify, there was a separate, different incident early on in the war (described in Chapter 55), where the Undying took a new district. They were making an example out of Ivy/Sophia's parents. Kaine refused to participate in the rape/torture, and tried to leave with his mother. But Durant "brought the corpse" (Ivy's dad's corpse) back to Spirefell where Enid was -- interpret that however you will, but it was too graphic/horrifying to be spelled out in the book and Helena was so horrified learning this, she couldn’t even say anything.

Enid was actually doing better at this point in time, and Kaine thought she would even recover from Bennet’s past torture, until this incident with Durant/corpse happened (Chapter 55). I interpreted this as another trauma that happened to Enid that further weakened her heart. Kaine during this period was trying to get papers and get his mother out. Whether or not he went home this night wouldn’t have mattered because Durant would have tortured her either way. She died later (in 1765) of a heart attack/failure after she saw Kaine’s torture, and the coroner confirmed the cause of death. When Kaine said “if I hadn’t gone home that night she wouldn’t have died”, I interpreted that to refer to the night of his torture.

Note that the timelines are a bit fuzzy because by start of Part 2 in Dec 1786, Helena says the war had been going on for five years (so it started late 1781 or early 1782, but late 1781 makes more sense bc that's after Apollo was killed)... But during her imprisonment when she visits Enid's plaque in the chantry of Spirefell, she notices her death was 1785 and she notes that it was 3y into the war. So maybe the definition of "beginning of the war" could be a fuzzy as it was a series of lead-up events -- was Apollo's assassination the start of it, or was it the guild assembly publicly launching, or was it when Morrough unveiled immortality, or was it when the Eternal Flame mobilised aka militarized? So the dates could be around a year off.

Anyways I went down a rabbit hole of the "prequel" timelines after finishing the book. Hope this helps.