Chapter 3: my sense of the mine was that if a fight broke out anywhere, the whole mine would be aware and charge the party. That was a bit much. Instead, I had the kobolds revolt. This is how I handled it. The sickly kobolds met earlier in the adventure were cured by the party's cleric. They were so thankful and enamored by him that he took the opportunity to convert them to the religion of Torag. Later, behind the scenes, those same kobolds went back to the mine to rally Hezle and the rest of the kobolds. By the time the party found their way to the mine, the revolt was in full swing. I set it up as an encounter of increasingly difficult waves of enemies as the cultists try to stop the revolt. I even introduced the party to Belmazog there as she had a duel with Hezle. She eventually was run off into the jungle by a rampaging mokole mbembe. The surviving kobolds hailed the cleric as a hero.
Chapter 4: the party found their way to the cultists' HQ very early in the book, before they had deactivated any pillars. They proceeded to find ways to get in. The ranger attempted to swim underneath the barrier. He became a permanent statue. Instead of having the player roll a new character, I dropped the hint that the elves might have a cure. The rest of the party then dragged his statue all the way back to the elves. They got dysentery on the way and ran into some drakes, but they made it and the ranger was cured and brought back to life.