Details on how I dealt with each of the story challenges (hope it will help someone achieve that perfect 7-kill run some day): 1) Caravan camp. I killed everything (2 wolves and 9 Glanfathans). Not much pacifism there, although I should have known better. 2) Cilant Lis. Sneaked around everything (started with 2 stealth as Orlan Cipher Dissident), including the treasure cache (for some strange reason, slime inside attacks 2 slimes outside, so you can easily loot the chest while they are dealing with each other). Had to "sacrifice" Calisca to get past the last spiders without a fight ("you must gather your party before venturing forth"). Oh well, she would die in a few seconds anyway... 3) Caed Nua courtyard. Pure stealth. 6 is enough, no special tricks. 4) Caed Nua Great Hall. Buy Bronze Horn Figurine before going there. Sticking to the left side, 6 stealth is enough to reach the point where script dialogue with the throne triggers. When it ends, doors open, and you are in battle. Just summon animat to keep these phantoms busy and run left to the stairs, you'll be fine. 5) Caed Nua dungeons. Pure stealth, no special tricks, although you'll have to avoid speaking to the ghost, otherwise you'll get out of stealth and attract some spiders. 6) Paths of Od Nua, level 1. Maerwald is quite tough, but who said you need to fight him yourself? Use a Fleet Feet potion to lure him out, then lure out some spiders and beetles from the other rooms and watch them fight each other - from a safe distance of course. Most probably it will end with Maerwald killing most of the monsters and then getting killed by the last 1 or 2 beetles. This will also likely leave the chest with the boots of stealth unguarded, which is great. If you are feeling especially mischievous, you can repeat the same trick with the looters slightly deeper on this level (they don't stand much chance against beetles). Oh, and don't forget the pesky xaurips - beetles will gladly eat them too if given the chance. Eventually, you'll be able to explore the whole level without any kills (I even got as far as level 5 without kills after upping my stealth a bit more).
7) Woedica's Temple. Easily done in disguise with Woedica's Hood, found on a body in catacombs just before (need stealth for that, obviously). 8 ) Sanitarium. Summon three wood beetles from Oaken Scarab Figurine for distraction, drink Fleet Feet, run for it. That's about it. 9) Heritage Hill. Stealth 10 is enough for the most part, but you'll also need a lot of summons for distraction: - 2 single summons (e.g. animat + beagle dog from Cloak of the Fox and Hunter) to go in and out of Icantha's house (also possible with a rite of walking shadows, but you DON'T want to waste it now). - 2 times x 3 wood beetle summons to run from the undead mob on second floor when descending from the tower (due to stairs script ruining stealth). Tricky, but possible. It also means extra rests to replenish Oaken Scarab Figurine (I rested twice just for Heritage Hill). 10) Cliaban Rilag. As I said before, you need stealth 12 (+2 hedge maze, +2 boots of stealth or footpad's hood, +1 Iquali's boon), mechanics 8 and lore 4 for this. And a rite of walking shadows. Use the rite just before the slimes in east corridor (guarding the door to the optional armory) and run for it as fast as you can. Once on the second floor, don't stop and keep running straight through the first locked door and to another leading to the machine room back on level 1. If you don't waste time, your rite will expire just after you pass that last door and get into safety. It's NOT EASY, but possible. 8 mechanics is needed exactly for opening that last door: high enough stealth can get you to the key, but you won't escape without a fight (even with summons). At least I couldn't. A rogue with Shadowing Beyond probably wouldn't have any trouble here at all. Of course, you'll also need to escape the dungeon via the west corridor after swimming through the underwater passage. 12 stealth is not enough here, so another animat distraction is in order. 11) Leaden Key ambush in Stormwall Gorge. Well, everyone knows this fight is optional with the right dispositions (I avoided it in my first run), but this time, I didn't have neither Benevolent=2, nor Honest=2, so they attacked, and I had to run around on Fleet Feet, eventually luring them all to their "accidental" death in the pungent embrace of some slimes and mushrooms. 12) Divine quests. Hylea and Rymrgand are easily doable with good stealth and no special tricks. 13) Burial Isle. Can be explored fully with stealth 16. In my final (successful) attempt at Thaos, I changed rest and brothel bonuses to something else, so I only had 13, and had to use another rite of walking shadows to get past the last group of ghosts. With 16, you can even stealth into that shortcut tunnel, but it will give you an injury, so why bother. BTW, I'm not sure what exactly does it check - dexterity and constitution don't seem to work (despite CON=17 being mentioned in some guide I looked up), perhaps it's athletics now? 14) Breith Eaman. The only problem is the animats guarding both doors leading to the room where we speak to Iowara. Even 16+3 isn't enough to get past them clean, so I used 13+3 (there goes last of the 3 rites of walking shadows) to get as close to the door (I picked the north-west one) as possible, and then, as you'd expect, the good old animat distraction trick (or even better, an adra beetle - it will live longer). It's still a bit hard there, doesn't always work well, but it works after 3 or 4 attempts. And these guards don't even detect you again after you get script-teleported to the center of the room for the dialogue. 15) Sun-in-Shadow. Easily done with stealth 13, except some optional bonus areas near the end. Thank gods, shadow drake spawns don't drag you out of stealth, and the second spawn even happens in the immediate vicinity of the exit, so, if you are in stealth, the game allows you to just leave instantly without pathing to it. 16) Thaos. Fight him. Such a shame that there's no other option, my char wouldn't really mind joining his cause...