Got a group who's been assaulting the Shadow Maze here ant there, been taking a few weeks [in game] to do so. Using the Amatatsu Seal. Dying. All that.
What's the fall out for this?
Is it weeks because they were waiting for the Seal to recharge?
Have they checked in on home? You could have the attack from the end of book 5 take place while the PCs are away - they come back and find the fortress in ruins. Various minor NPCs are dead. (The most important ones have fled, but the PCs don't know where until they've searched the place for clues.) So instead of defending the fortress, the PCs are assaulting it, and the Oni have brought in a couple of extra lines of defense.
Good idea and to answer your question:
Weeks due to resting, travel times, and waiting for spells like restoration to become available to them again.
Is Yugureda never going to be any closer to fixing his situation? As in, if it takes the party three weeks to clear out his island and assault his home, does anything change for the final encounter with him?
Up to you. It may be that what Yugureda is trying to do is impossible without deity-level magic.
You could just have Yugureda better prepared when the PCs turn up. I boosted the encounter by adding a few more undead to it.
The adventure assumes you successfully rescue O-Sayumi and she arranges a meeting with Sikutsu Itsuru but if her soul is lost forever you could have that meeting happen in another way. The PCs could fail to make an alliance with the geisha, costing them rebellion points in book 6.
Alternatively, O-Sayumi's soul could end up in Tarukimi's aged body, and vice versa, and the PCs would have to persuade O-Kohaku that this still counts as a success.
I kind of figure if the PCs can undo the magic jar effect, he can, too, and possibly restart the entire process.
Penalizing them for taking a long time is not so cool, but insisting that there's urgency by changing the outcome in ways you've suggested is more in line with what advice I'm looking for. Thank you.