If intelligent aliens existed, would it be our duty to treat them the
same way we treat fellow humans?
Some philosophers such as Ayn Rand say that it's not a good idea to think about morality in terms of duty. Duty is often used to denote something you are supposed to do despite having criticisms of it: it is a demand that you should act irrationally. What you should do is work out what is in your rational self interest and do that. It may sometimes be the case that your rational self interest is served by entering into an agreement and fulfilling its terms, e.g. - getting a job and fulfilling the terms of your employment contract.
If aliens can create new explanatory knowledge then we may be able to gain something by cooperating with them. In that case, we should apply to them the same moral standards as we would apply to humans.
What about if they were killing each other off? Would it be our duty
to intervene? If their culture espoused torturing one another for
pleasure, should we then intervene?
We should advocate good ideas. Intervening in other ways might be a good idea depending on the context. If some of the aliens resist their bad culture then we might want to help them to escape, or even use force to stop their mistreatment depending on the circumstances.
Are our morals truly Universal, or do they apply only to humans?
Good moral ideas are universal. But I don't know what moral values you hold or whether they are any good so I can't say much about the applicability of your moral ideas.
If these aliens attacked us, would we be justified in any level of
brutality during retaliation, or would we be morally required to offer
them the same legal protections we offer ourselves?
We should apply the same moral standards to the aliens as to human beings. Dropping bombs might be a reasonable way to wage a war even if it sometimes kill civilians. Raping aliens wouldn't help win a war and would be evil and stupid.
Is it possible that other intelligent life has what you may refer to
as a "soul?" Or, despite their intelligence, are they mere beasts by
default? What level of intelligence requires us to treat them the same
way we treat humans?
If the aliens can create new explanatory knowledge we should treat them as people, otherwise we should not. If they can create new explanatory knowledge we can engage in trade for mutual advantage if we and they follow the appropriate moral ideas. If they can't create new explanatory knowledge then they can't learn or impart good moral ideas, nor can they learn or impart good ideas of any other kind. Treating them as moral agents would make as much sense as treating you car as a moral agent.
The idea of a soul doesn't make much sense. Thoughts are abstractions but they always have to be instantiated in some material. The difference between humans and animals lies in the ability to create new explanatory knowledge, not in anything supernatural.
You might find it useful to read "The Beginning of Infinity" by David Deutsch.