Your heuristics are a very close match for my own. I've written similar options in previous threads here concerning flagging and the ranking algorithm.
Whenever this matter surfaces, I recommend the HN Slapdown user script [1] which indicates stories that have been moved below the position they would have based on points only. In other words, it draws attention to stories that have been flagged or otherwise adversely affected.
In my opinion, the homepage either weights non-upvote inputs too heavily or receives too many non-upvote interactions from users.
I can't be certain whether flagging or other measures such as the "flamewar detector" are more or less responsible for the volatility of the home page ranking. My only anecdotal evidence is that when I have (very rarely) flagged stories, I've witnessed an immediate and severe rank adjustment, often immediately sending the submission into second-page purgatory. This has given me great respect for the severity of flagging.
My heuristics:
1. Most of all, I try to keep my interactions positive. If I don't agree, I act as if I don't care, by which I mean I do nothing. I see little value in downvoting something I disagree with. It won't change the person's mind—only a comment in reply has a chance of that.
2. I will downvote comments that I believe are objectively wrong and potentially misleading to other readers or are clearly intended to be offensive or mean-spirited. Still, I feel I am very sparse with downvotes. I downvote approximately one out of every 1,000 comments I read.
3. I've only flagged stories that are unrelated to technology, but even then only in extreme cases. I don't bother flagging stories about popular fiction, movie reviews, or other elements of geek culture because I don't think those stories are an epidemic at HN. Like you, I feel it's important to leave a comment when flagging a submission. I have flagged two stories if my memory serves me correctly.
4. I skim the new section on every visit to site; about once per day.
5. I upvote stories I find interesting or agreeable. I think this is the point of the upvote. Upvotes are where I can be entirely subjective. I upvote approximately one out of every 10 stories I read.
6. I upvote comments by the same rule as stories. I upvote approximately one out of every 100 comments I read.
7. I strongly disagree with downvoting or flagging simply because of disagreements. I don't think use of downvoting is as problematic at HN as elsewhere (e.g., Reddit), but I do feel there is still slightly excessive comment downvoting and moderately excessive story flagging (or other adjustments).
[1] http://userscripts.org/scripts/show/150452