[sblock]Chapter 3's War Council actually went really well. I thought it'd be dull for them w/ all the NPC text, but I planned all of it out beforehand (adding and/or modifying some of it) and it was pretty easy to think of replies to the PC's statements on the fly.
The sidequest with the abducted girls was the one thing in chapter 3 the party seemed really interested in, so I fleshed it out quite a bit. Some of the party visited a brothel and found out that rich halfling owned it though he left it in the management of another person, and also visited Paradim's shop and wondered what he was hiding. The party's ranger then staked out the back of the shop at night and saw some dark-clothed goons like the ones at the brothel deliver some drugged young women to Paradim, so he could work his magic. After they left, the ranger decided to confront Paradim solo rather than get the whole party first. Figuring he'd have cowardly traits and she'd gotten the drop on him, I just had him Wayfarer's Step outside and flee. The party got tired with the chapter and lost interest in the sidequest a while after, so Paradim's whereabouts went unresolved (I did have the authorities arrest the halfling crime boss in the chapter epilogue...original plan was to have the party take him down, but oh well).
That left me a lot of creative room on what to do. I decided what happened behind the scenes was he fled to Lee in desperation (losing the girls meant the halfling would probably have him killed) and wanted to arrange an ambush on the party to kill them, but Lee still had a soft spot for Torrent and hoped to avoid coming into conflict with the party, so instead Paradim fled town for Ostalin, to continue his work in Pilus's lab.[/sblock]
As for why Chapter 3 went so poorly...I'll save that rant for if I review the campaign. It's in the past for you now as well.
Chapter 5:
[sblock]The first thing I do when preparing for a new chapter is list all the encounters in rough order of occurrence, including ones that may not happen, with the CR/EL. I like to figure out at what point the party will get their mid-chapter level up, and if that is problematic. Namely...they need to rest to level up, and many chapters have a habit of dumping a TON of encounters in a single day at the end when the players must run a gauntlet, so that might necessitate giving out the level up early.
I immediately noticed Chap. 5 is bereft of encounters, even if you count on the unlikely optional ones (like taking on the 100+ Ragesians, or taking a swing at Pilus)...which also had some of the meatier EL values. This is compounded by 1) the fact that they spend a great deal of the Chapter parked in Eresh where having random monsters wander in is hard to believe and the fact that they'd get hit w/ Balance's boon and 2) most of the encounters happen during the Valley of Storms trip and the valley and lab are the only logical places to cram in more encounters after they reach Eresh, other than maybe some more Ragesian fights during the battle. Also, the party's supposed to level up before going to the valley (and the fights are tough, so they should)....so while it's presented like the valley can be done before the Ragesian army battle, it really can't w/o modifying the foes.
The chapter's just...logistically tough. You also need to be very careful about the order of things happening and how much free time they have, lest you're comfortable with them possibly deciding the best option is to force their way into the monastery, make them take in the townsfolk, and demand an audience w/ the brothers. I didn't want to deal with adjusting for that, and then the valley can quickly start to look like a pointless excursion to the party (they're just there to get the orb and maybe save the townsfolk from Ragesia). Even replacing the many lost encounters w/ fighting the monks, I really think the party should see what's going on in the lab before getting a chance to ally w/ Pilus, they should be able to see he's hiding a lot.
My solution to get through the chapter mostly boiled down to railroading them so hard they didn't even realize they were being railroaded.

I added some wilderness encounters on the way to Eresh to bolster their xp. Once they arrived, events happened so fast, they got caught up in the rush of it all and it went smoothly. I think they spent all of 3 days in Eresh (doing everything there and fighting the returning Ragesian army) before going to the Valley of Storms, maybe it was more like 2.5 days. There just isn't much to do there, and the more time they have to putz around, the more they'll get frustrated with the monastery being closed off.
One thing I did w/ Balance's death was make a list of different emotional spell effects (Good Hope, Crushing Despair, Mindless Rage, Fear, Hideous Laughter, and (from Pathfinder) Unnatural Lust...by far my favorite) and roll randomly to see what would affect a party member that failed the will save (and for the town at large, but I wasn't going to do all those rolls!). Lead to some hilarity and plenty of chaos. The party's effects lasted a few minutes, many of the townsfolk's lasted much longer (proportional to how long you'd been under Balance's calming boon), giving some encounters for the party to try and settle things down.
Before Balance perished (and, ironically, contributing to it), some troops from Duke Gallo (he got along very well w/ the party and the party's druid ended up in a romantic relationship w/ him) arrived to help and drove off the Ragesian camp on their way there, and the party managed to get some monks to disobey Caela and join in the defense based on the party's impassioned pleas, and I did an war battle like in Otharil Vale (I made my own subsystem for it), though this time w/ the odds stacked against them. I decided to let them level up before the battle even though it was mid-day (they could add new spells and daily resources but expended ones were still gone and already prepared spells couldn't be changed) upon realizing that if I didn't, they'd spend all of level 10 just on the Valley of Storms arc. And just in case they lost the battle and had to engage in regular fights against enemy waves, to give them a little boost.
They also had really bad luck, so they lost the battle convincingly (specifically, while they were losing in the direct combat as well, an enemy scout unit snuck into Eresh and set it on fire, causing and instant loss as the party's militia army broke in a panic...basically the fighting was south of the town and they had to prevent enemies from getting past the river into town while either wiping out the enemies or routing the general's unit). Eresh is engulfed in flames and fighting continues in the streets as the scattered and worn down party members have to reunite and then survive several waves of Ragesians before taking on the general's retinue. Midway through, some Two-Winds Elementals joined the fight to aid them, to the party's relief. After defeating him (and the Ragesian army retreating in response), they were severely weakened and as they were about to heal up, they noticed Torrent oddly quiet on the ground, writhing in pain, being grappled, pinned, and mouth held shut as a gang of invisible stalkers beat her unconscious. The Two-Wind Elementals stated it was time for the second phase of their orders, and turned on the party.
Once Torrent was out cold, the stalkers met the elementals in the air and handed her off so they could fly away at the "you can't catch me!" speed of 100 ft (perfect)...cause invisbile stalkers flying away at speed 30 and expecting PCs not to keep up is pretty foolish, and having the turncoat elementals betray the party just felt so right. The party tried in vain to chase after them before collapsing from exhaustion of the brutal day they just had and waking up the next morning in the healing house, eager to go rescue Torrent.
From there...they went through the valley, I added some Phrenic owlbears and an encounter with a severe lightning storm they had to find shelter from. In the lab, a major image of the invisible and pre-buffed Paradim greeted them and called forth Aurus. They found Torrent in a vat while fighting through the complex and after winning (Paradim fled...again!) but without her equipment. They find it in the study and explore the room while she hastily gears up (I changed the carpet trap to one Caela could activate remotely as an action, rather than have it go off when they walked in and poor Torrent was still without her stuff) and then Caela gives her spiel and attacks. The rest of the chapter went as written. I had a whole plan for if they attacked Pilus, but they decided to make a deal with him.[/sblock]