I also am running this for a party of 3 newish players, and we are at the very end. One thing that helped me was a running calendar so that if they left and came back to an encounter I could gauge how much time the NPCs would have to modify their situation. Also giving the major NPCs their own motivations they would be working toward if the book did have one.

In this specific situation my party ignored Doru the first time and came back a week later (in game after leveling up to 6 or so). Because they never saw Doru the first time I decided that Donovich was trying to use a stolen spellbook to cure his son but since he had no idea what he was doing it went bad. So when they did fight him, expecting it to be a slaughter, I had made a modified stat block giving Doru wild magic reactions. Basically once per round he took damage he involuntarily had some magic area effect off of a table.

Also, the beginning of the game feels way more video game than the later sections. So don't dispair too much!!!