It doesn't end I don't think, it tells you 2 different things. his book says he was just on the cusp of making a great discovery with it using a 4th stone, which I can't find ANYWHERE. But then if you interact with the scroll on the floor by his body, it tells you the correct way is that it spawns a Boggart.
I spawned one and I had to turn on aggressive mode to attack it, and that gave me a 37K bounty crime for killing it. The quest didn't go away either, and I can't spawn any more Boggarts.
So for the puzzle itself, I can't remember exactly, but the purple stone goes in the southern one. Just try blue/red in the other 2 and swap them around if it doesn't work.
So I stumbled upon the guys note as well. Managed to order the stones correctly and summoned the boggart. The quest didn't go away and I didn't know what to do so I thought I'd jump on here and see if anyone else did. Seeing you guys were in the same boat, I figured I'd come back to it later. So I ran north to finish the quest I was originally on, ran into some enemies and noticed the boggart was fight along side me! He also warps with you, even into towns. Now I'm wondering if there are going to be any other creature allies. Hope this helps.