As a fellow non-moderator, I cannot view most flags, nor any deleted comments. But from what I can see from your description here and the comments and status of the question, I don't think you've even remotely approached overstepping your bounds. Basically: you're fine.
I think in your initial three-item bulleted list here, you've actually enumerated four kinds of things you'd communicated about: (1) suggesting a question should be closed as a duplicate; (2a) voting and (2b) critiquing an answer with a comment; and (3) requesting information/clarification of a question, with a comment.
The community as a whole, rather than moderators specifically, are responsible for all those things. By doing them, one does not create a particularly high risk of accidentally stepping into the shoes of a moderator inappropriately. As Jorge Castro says, "the site is community moderated[.]"
Three of these four things--(2a), (2b), and (3)--aren't merely not moderator jobs, but are actions that mods don't even have greater power to do than regular users.
Technically, I think moderators have less restrictive rate-limiting on posting many comments in a short time. But since users with the comment-everywhere privilege can do so about every fifteen seconds, at least for a while, this is an insignificant difference in terms of what it says about the role and authority of moderators.
As for identifying and acting on duplicates, it is true that the system gives moderators a special power in this regard: they can close (and reopen) any question with a single close (or reopen) vote. However, as you may have noticed, this power is not usually used to its fullest: except in cases where a question is "blatantly off-topic" or its merits/problems are unusually clear, or when the close queue is filling up so fast moderator help is needed to control it, I've observed it's rare for moderators to cast the first close vote on a question.
More importantly, moderators' binding close and reopen votes don't represent a final authority to decide which questions are acceptable. Questions closed (or reopened) by a moderator can be reopened (or re-closed) by the community just as easily as questions closed (or reopened) just by community votes, and this really does happen. In addition, questions' status can be discussed on meta. There is no obligation that we agree with moderators about what questions should be open or closed (nor, in general, that moderators agree with one another).
In one comment, I believe you might actually have made the opposite mistake of what you're concerned you may have made. (But it is not a big deal in this case, and I don't think it requires correction.)
I think this is a duplicate (we'll let the moderators decide) ...
That's not really how the site works. The community decides what's a duplicate (and more generally, what questions to close). Some members of the community are intended to have and regularly exercise more say in that: users with 3000+ rep. 3k users are encouraged to cast and review close votes; in contrast, mods try to do so sparingly. The Stack Exchange philosophy that underlies moderator action is that its focus should be exceptional situations. Ask Ubuntu is not ruled by moderators.
Let's look at the other extant comments:
-1 although it is in the repo, that version is not up-to-date (so this answer is incorrect I'm afraid)
sorry I wasn't clear, that version doesn't work (I forget the details at the moment, but I know this is why I myself use the PPA instead)
Nothing in these would suggest you hold any special status or authority on the site; these are the sorts of things anyone could say. They're perfectly polite too.
(Personally, I rarely put "+1" or "-1" in a comment, because I want my comments to be about the post and not about however I've voted. But plenty of people do and there's nothing wrong with it. Certainly you're not overstepping your bounds here--many, many users can vote a post down.)
your question says you tried the PPA version, do you know what you did differently this time?
hmmm, so the ppa error was unrelated? is it possible that this question is then a duplicate of askubuntu.com/questions/167431 ?
There, you asked if an author knew something related to their post, and suggested that a question might be a duplicate of another one based on information that had been provided, including information provided in reply to your questions.
That's definitely fine. Even if you were mistaken (which I don't think is the case--I did vote to close the question after all), this is still normal helping behavior of precisely the kind we wish to encourage.
So basically: you're fine. Not just fine. Good.
In this meta question, you mentioned:
FWIW I don't intend to make a habit of this ...
How much and in what ways you choose to contribute to the site is of course your decision. But I hope you do continue helping people improve their posts and seeking to point out misinformation. Far from being undesirable or something that is tolerable only in small amounts, these sorts of actions are necessary for Ask Ubuntu to continue functioning and helping people.
So please feel free to keep up the good work.