Timeline for Factol Darkwood

Nope, it was activated. But it's the party of PCs in Faction War that got the result of the spell, not Gifad. Essentially, all the spell could do was give them a one-word Wish-type effect to "reshape" Sigil in a subtle way. They're slightly nudged towards using the word "Peace" or something of a similar manner to end the Faction War that was raging through the city at the time, which as described wouldn't be a sudden massive effect that would force everyone to stop fighting but would instead would lead to a slow cooling of hostilities in such a subtle manner as to cause the party to question if the spell actually worked at all. And I don't believe the effect continued on past there in making Sigil a peaceful place in canon (though it certainly would be a reasonable choice to make in your game). But it leaves open the possibility for them to use anything so long as it's just a single word. There's some degree of impact in the intent of the word too beyond just the straightforward meaning. While it says the party's intent being to end the Faction War aids in focusing the impact of the spell on just that conflict, it also mentions other possible alternatives like "order" having potentially unintended side effects due to connotations of the term.

According to the ending of Faction War, she did it out of a sense of twisted irony and amusement to pay homage to the three universal laws: the Rule of Three (three incarnations of Darkwood), the Unity of Rings (obvious), and the Center of All (Darkwood was at the center of his goals the whole time. Not just that, but as soon as Darkwood was trapped within the gem as the mage, the Lady restored both his sanity and his memory specifically to force him to have the awareness both of what he'd done, how everything was his own fault, and how his ultimate fate was to be released briefly by himself only to be obliterated by his own ritual.

It sounds like you might have missed part of the conclusion, Palomides. Pages 110-111 goes over the results and effects of Darkwood's spell, and the epilogue on page 112-113, the second page in particular, goes over Gifad's fate as the mage in the distant past.

The first time a "Rowan Darkwood" appeared, in the Treasures of Greyhawk anthology, he was listed as lawful neutral. It's not completely clear this is the same as the Rowan Darkwood who appeared as a chaotic good ranger in the Planescape boxed set. "Gifad," the Oldest Barmy, was listed as chaotic neutral. I'm not sure there's any reason to assume the Ancient Wizard was evil.

See below.

Well, some problems with that:

- Vecna is still active and "alive" (a living god, though undead) today. The ancient wizard was destroyed when Gifad activated the soul gem.

- The ancient wizard was imprisoned in the Labyrinth Stone well over 10,000 years ago. Vecna's battle with Kas was only 1,000 years ago, during the period when the wizard was imprisoned in the Labyrinth Stone, somewhere in Pandemonium. The timeline doesn't match up, unless you're suggesting that at some point he time-travels to the future, becomes a demigod and then a lesser deity as Vecna, then loses his divinity (because the ancient wizard was physically in Sigil, which is normally impossible for a deity - Vecna admittedly found a loophole, but it seems unlikely this would work more than once), travels back to the past at some point in the future to confront the Lady (seems unlikely, since the book implies he confronted her at the height of his power, whereas for Vecna this would've been several steps down) and got himself caught in a gemstone for tens of thousands of years, only to be annihilated by his past self.

- The ancient wizard was Rowan Darkwood. Rowan Darkwood's circuitious, nonlinear life is pretty well accounted for. He was busy either being Rowan, or locked up in the Gatehouse for centuries as the Oldest Barmy, or locked in a gemstone in Pandemonium during the times Vecna was active.

- Other than sharing a homeworld and being wizards, Vecna and "ancient wizard" Gifad/Rowan have nothing in particular in common. Oh, I guess they both lost an eye, but under very different circumstances. Rowan lost his to baatezu torturers, while Vecna lost his to Kas's sword (or to priests of Pholtus, if you follow the comic book). And Rowan has both his hands.

- Oerth has a bunch of other ancient wizards on it, anyway. Even evil ones. There's Kyuss (a cleric/wizard/true necromancer), Shattados, Drokkas, Asberdies, Ohjos, Oolan, the Ur-Flannae wizards who attacked the City of the Summer Stars, and Keraptis, for starters, so Vecna isn't necessarily the first place I would go. Of those, Keraptis is the only one known to have undergone anything much like time-travelling, but we know how his existence ends, and it's very different. Well, Vecna definitely attempts a time-travel-based plot in Vecna Lives!, but it fails, and again the timing seems off. Theoretically he might have traveled forward in time to whenever Vecna first started rising to power as a lich (4,000-2,000 years ago, maybe), gotten vaporized by Kas about 1,000 years ago, spent centuries rebuilding himself as a demigod, imprisoned by Zagyg (it's implied) about 90 years ago, freed around 25 years ago, had a showdown with Iuz around 15 years ago in which he was lost on some unknown plane for five years or so before being imprisoned on Ravenloft for another ten years or so... that lost period could've had him sent back 20,000 years or whatever, but he still would've had his divinity, and things couldn't have ended for him then, because he still needs to be imprisoned in Ravenloft. No, I'm not seeing it, though if you really want to have Vecna's destiny to be to end as a disembodied voice in a gemstone killed offscreen by Rowan Darkwood activating an ancient spell... more power to you. Might be disappointing to the players, though.