On another note, I do not think that Voldemort left Quirrel for someone else, he still seems to be controlled by another being most of the time, even if there are less visible marks.
Yes, I don't have any ideas about zombie-Quirrel/lucid-Quirrel, or Harry's sense of doom around the latter. Does any of that exist in canon, and if it does, what's the story there? I'm only familiar with the general ambience of the Potterverse, not having read any of the books or seen the films. (Spoilers welcome, I don't intend to read/see them.)
Here's an idea about the sense of doom following on from V having tried but failed to possess Q: Harry's scar is a piece of Voldemort (doesn't canon have the scar being a horcrux of V?), and the sense of doom is the Voldemort-fragment's fear that Quirrel might discover and destroy it.
Quirrel has spoken of at least one past experience that appears to have been Voldemort's (killing an entire monastery because the master wouldn't teach him). So, maybe what we are looking at is a Quirrel/Voldemort merging, in which Quirrel is in control (except in zombie mode), and the Voldemort-fragment reduced to nothing more than memories.
The sense of doom may just be a filled-with-fantasy Harry brain's interpretation of the Voldemort-emotion/proximity as opposed to the pain that cannon!Harry felt. MoR!Harry already has a far different view of things due to his fiction reading (just look at his interactions with Hermione), why not a different mapping of an unnatural sense?
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.