How about Thousand Bones says a spirit from beyond won't rest until it has a chance to impart its greatest secret to those still living. The spirit is that of Neolandus, and after Thousand Bones conjures his spirit to talk to the PCs, the shaman can then put them on the trail of the Sun Shaman, etc.?
Yeah, assuming you're not worried about leveling at all or are otherwise taking care of it, they can just get the information from a now dead Neolandus (and prob Vencarlo, also hinted at during the Neolandus séance), and in the middle of their return to Korvosa at the end of book 4, try to tackle the Emperor (and maybe the Arkonas) again.
Also, the information that Neolandus was going to give the party is confirmable with a DC25 history check, so you could potentially have given them a chance to piece the basic importance of the Shoanti/Sun Clan together while they were in transit.
I agree Neolandus' ghost is the best way to impart this information. You'll need to account for the Shoanti obstructionism, though - one of the common criticisms of Book 4 is that the Shoanti make you run around on a huge poorly-motivated fetch quest to get the information you need. It's worse if you don't even know what information you need or why, so you might risk PCs just disconnecting ("OK, the Shoanti are too needy, let's try Magnimar for a Reincarnation spell").
I'd suggest giving the most divinely linked or psychic PC a dream sequence / divine vision of Neolandus' spirit frantically trying (and failing) to tell them something, selling the impression that his information is vital, and only Shoanti Ritual X can get them in contact with him. You could even have the Shoanti be ignorant of the truth - the stories have changed in an oral tradition over the years - and only Neolandus can see and reveal Scarwall's nature from beyond the veil. When I ran it we changed it from "The Shoanti refuse to tell you unless you jump into Cindermaw's mouth, fight this monster, go here, lift this, etc" to "The Shoanti can't tell you, but to contact their spirit ancestors who know the truth, you'll need to conduct the SHoanti ritual which involves jumping into Cindermaw's mouth, fight this monster, go here, lift this, etc".
You'll also need to level the PCs up more, or the Cinderlands will mash them.
Looking ahead to the fallout further into the future when they return to Korvosa later:
- Vencarlo is dead, and depending on how much they found out about his secrets, Blackjack is dead with him. Perhaps the Arkonas leave Blackjack's body publicly hanging, showing that the hero is dead, making the city lose hope, and clearing the way for 'new hero' Triffaca.
- One Arkona might succeed in killing the other one off screen. Pick who you like better of Bahor or Melia.
- One of the Arkonas could be shaped shifted into Triffaca - or even into Blackjack, cutting Triffaca out of the story entirely.
- One of the Arkonas could be shapeshifted into Neolandus, who has publicly returned to affirm his loyalty to Queen Illeosa (Bahor having reached a backroom deal to support her, while the pair plot to ruin each others plans). There's some fun to be had in the party doing a quest to speak to Neolandus' ghost... only to return to the city and find him alive and well.
Edit: Darn, looks like you've already got a plan in place! Nevermind my suggestions then! ^^
Allow me to offer an alternative option, particularly if the PCs haven't even really gotten the idea that Neolandus is still alive and a prisoner somewhere and so his spirit showing up is just going to be "weird old guy who knows an awful lot and looks like that Senaschal guy who died at the start of the campaign, maybe?".
Neolandus's effective contribution to the entire campaign is to point the PCs in the direction of the Shaonti, and tell them that they might know something about Ileosa's strange immortality powers. Your group is already headed there, so all you need to do is twig them onto the fact that the Shaonti might know something important about the queen and how to defeat her. Presumably they've already seen/heard about Endrin's disastrous attempt at regime change and that Ileosa just shrugged off a crossbow bolt to the head, so they know powerful plot magic is on her side right now. Given they already decided to get out of the city for a while I will assume that they're looking for more help with this than just reviving a dead NPC party member. So, hopefully, if you toss them a life line of some sort they'll grab hold of it and you can just pull them back up onto the plot from here.
Since they already know Thousand Bones and did him the favor of returning the bits of his dead son back to him in Book One, he's already willing to help them. He brings the NPC party member back from the dead in a sort of "life for life (body for a body?)" exchange (hell, maybe even his son is back up and kicking and that's what Thousand Bones needed the body for). It seems more fitting with the Shaonti that this would be a reincarnate rather than a Raise Dead as druids seem like a better fit than cleric, but you're the DM here so make changes as you deem necessary!
If this dead NPC party member is Laori Vaus and not an original character (since raiding the Emperor's palace would be around the time she shows up in the plot), then it's pretty simple from here. She feels that she owes the party for reviving her, and so shares the *real* details of why she's in Korvosa, at least in so far as that she is member of a Zon-Kuthite sect known as the Brotherhood of Bones seeking relics of the ancient warlord Kazavon. She believes Ileosa has one such relic, and that she got it from the ruins beneath Castle Korvosa, ruins which the Shaonti were guarding for centuries so maybe they would know more about it? Given this is Laori Vaus, I imagine she wouldn't have paid super close attention to all of her sect's lore and so might be fuzzy on the details, such as Kazavon was a dragon, if you want to save that reveal for a dramatic moment later. And she wouldn't know important plot details like the party will need to go to Scarwall next to get Serathial to stop Ileosa, saving those details for the Shaonti to impart so there is still reason to do Book Four. But hopefully she can provide enough exposition to fill in for Neolandus.
If said NPC was a permanent party member who has been with the party since the start and Laori Vaus is still alive and well, perhaps she's abandoned the plan of interviewing Korvosa's artists to get more information and has moved on to trying to talk to the Shaonti, and thus is there with Thousand Bones when the PCs arrive or catches up with the party in Harse to travel with them to Thousand Bones, thus giving them a bit of support to actually survive crossing the Cinderlands and *get* to Thousand Bones.
Or, instead of Laori, you could always introduce Sial here instead, conducting an investigation outside of Korvosa while Laori continues mucking about in the city. Perhaps he's heard of the PCs through Laori (if they had a pleasant enough first meeting prior to the abortive palace raid), and so knows who the PCs are and is willing to help/ask them for help with convincing the obnoxiously stubborn Shaonti to spill the beans on what they know/do a mutually beneficial exchange of information - he wants to know what they know about Queen Ileosa, and is willing to offer some backstory on what his theory is for the queen's newfound powers (that she found a piece of Kazavon).
As for ensuring that the party catches back up on experience, you can always give them some road-side adventures on their way from Korvosa to Kaer Maga and then the Cinderlands beyond. Maybe they get caught up in some of Trinia's misadventures around Harse rather than those happening completely off-screen, and given they've already helped her out once the PCs feel obligated to stop and help her out of yet another jam - or perhaps helping her to loot some dungeon she found outside of Harse.
Depending on how the party feels about House Arkona, you could even have this dungeon be some sort of summer villa they have outisde of the city in the countryside, which of course also hides some grisly details of what they really are inside the villa, along with ancient traps and guardians. Hell, if you want to give them a second chance to save Neolandus, just move the Vilified Labyrinth to the basement of said villa - the Arkonas wanted Neolandus far away from Korvosa, and they put their murder dungeon under the villa far away from the prying eyes of the city.
That gives them a second chance to save Neolandus (by accident basically), but still maintains a consequence for their earlier cowardice - Vencarlo Orsini was held at the main manor in Old Korvosa, and thus is dead, or dead (but impersonated by a rakshasa), or if the party liked Vencarlo and you want to keep him around, he gets brainwashed into being an Arkona hitman. Maybe the party saves him too when they come back to the city, or maybe they're forced to put him down.
As a final alternative, you can just throw Book Four out entirely because you find the Shaonti series of fetch quests obnoxious or think your party just won't go through all that for some nebulous information the Shaonti may or may not have. That does leave you with needing to create more of your own material though, but I could certainly see the potential for an alternate path to Scarwall here patched together from the party undergoing arcane studies in Kaer Maga using the libraries there, possibly in conjunction again with Sial/Laori investigating Korvosa's past. Which could also still involve going to some of the encounter areas out in the Cinderlands anyway, such as the Arcopolis.
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In their initial encounter with Laori, the paladin (a half-orc who instantly recognized the holy symbol of Zon-Kuthon) did an immediate "Detect Evil and attack" response, scoring a critical and killing her within a single round.
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*Half-orc paladin of Sarenrae
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That's a pretty extreme reaction towards the follower of a Lawful deity from a Paladin of the NG goddess of redemption.
With those sort of reactions, how does this paladin even survive in Korvosa - considering that the third biggest (and most definitely legal) church is the temple of Asmodeus?
Killing LV on sight alone is not only barbaric (verging on evil), but illegal too. Is this Paladin still a Paladin?
I love paladins, but pretty much 90% of the population play them and lawful good wrong. I really wish they did not have detect evil just to prevent this from happening.
The Paladin in my home brew game used detect evil as some guaranteed compliance with killing every “bad” person they came across. I finally had to take the Paladin class away from him and change his alignment. But this and lawful good always broke out into arguments at the table about what it really means. It did not help that this player always plays “chaotic good” with a heavy smattering of neutral evil mixed in.