I don’t really remember the Begain Island quest, I think that’s optional. You don’t mean The Isle of Bigail, the Anama/Cockroach island, do you?

I dunno, are you supposed to ever get through the gorge through the mountains in Krizsan Province, killing the group of troglodytes?

Are you talking about the ones near Fort Emergence? Regardless, if it’s a fight then you should be able to clear it eventually.

There’s not quest to bring down the Anama or anything. You can join them if you want. You won’t be able to cast mage spells, but everyone will get a huge bonus with priest spells and learn spells for free. If you try and learn mage spells after joining, they you lose your membership. There was a way around this in Exile III, I don’t know about Avernum III: If you joined the Anama and then raided their treasury, you could keep your Priest Spell boost but study mage spells again. HOWEVER, the entire city of Shayder would then be hostile toward you forever, and everyone would attack you if you went in the city.

You don’t need to join the Anama, it’s optional and you probably don’t want to mess with it.

I don’t know if this counts as a spoiler but if it is then it’s a minor one: to beat the game you’re only required to stop the roaches OR the slimes, not both. I think the roach plague is harder, so if you did that already then just go ahead and do the slimes, it will be good XP. Once you stop a plague, the towns in that province won’t receive any further permanent damage.