So I continued onto the alchemist's cave to fight the shaman, and I cant get past him at all
1. Please, explain this, I don't understand. Is he too strong for you or is he frozen on the spot? You don't kill him right away, but work him down to a few hit points, then you are kidnapped by him.
2. Which patch version are you playing and when did you patch to 1.45?
IIRC in the unpatched version teleporting yourself to the BF without having the fragment brought you back to imp village, so you did not complete the Necro task. And IIRC correctly again, this had no impact on the game (you just lost XP). But you did pick up the Bafflimiri mushroom? This is crucial for the alchemist quest.