When you see the toad shaman for the first time, after getting in through the front, saying Ukabu, etc. He tells you there is a great evil that you must help him with, what is the evil and how do I get rid of it, and what do I do with the toad potion? Going back, I never found out what an Ukabu is, what is it?

go through thr hole in the floor, and make your way outside

Where exactly is the hole?

if you are in the shaman room hole is in the room with you.
the potion goes to a toad that wanders near the windmill with the spider in it
That toad is where you learn the word ukabu from

Is it in any way neccessary to talk to the villager near the tower with the spider? I had a problem with him and another villager getting stuck in a passage, so I killed them in one shot without alerting the other toad people. I noticed the trap door, but it says it's not working.

I restarted the whole thing, did the same things, and it worked. There must've been a bug in the game.