Questions should really only have one part. There should be one underlying question, which is what the title is about. That isn't to say that there can only be one question, but all the questions should be closely related (enough that someone who could answer one could also probably answer the others), and they should all be about the same thing. The difficulty with multi-part questions is that they aren't easily searchable, and they are harder to answer completely than if the question was split up.
I'm not knowledgeable enough in this case to tell whether these really are different or if it makes sense to bundle them together. However, in general, if you find such a question, you should ask the OP to edit the question to be more focused (as you did). If they do so, then the problem is solved.
If the OP doesn't respond after a reasonable amount of time (at least give them a few days, or until the next time they log in), it's a tricky business. I'd suggest closing it, then editing the question to be more focused on the title question. After reopening it you can answer that. Closing it really is a formality if you want to answer the question, but it's more acceptable to make fairly drastic edits like this to closed questions IMO. If the other questions in the post are also worth answering, you can post them as separate questions and answer them yourself (and add a comment directing the OP to those posts as well).
It's possible that the OP might come back much later and complain about this. However, if you gave them enough time to edit it themselves, and they didn't, then they don't really have much right to be complaining in my opinion. This is part of what makes Stack Exchange sites different from other fora: we value the content more than the users. By salvaging their their post you are doing both them and the site a favor. If they have a problem with that this isn't the right site for them.