I am in the process of making my first batch of homebrew, specifically, I am making a porter. This batch did not take as long to ferment (only 6 days) as what I understand is normal (1-2 weeks).
That's probably okay. For small to regular beers with good yeast, the primary may well be 3-7 days. Does the beer taste sweet-worty? Racking to a secondary fermenter is useful at this point to remove trub and allow for clarification and maturation time without picking up off-flavors from the trub. You can stay in primary and just go by visuals if you wait until all the kraesen is gone and the yeast is well settled out before bottling. SG readings (as you mentioned), samplings, and generally more experience will help you learn more precisely when to rack or bottle.
Unfortunately I could not determine that it was done by means measuring SG, as I did not have a beer thief/hydrometer when I started (I do now), but the bubbling of the airlock had definately stopped at that point. So I went ahead and racked it to a priming bucket, added corn sugar primer, bottled it, and stored it in a dark, room temp (70F-75F) place. It has been carbonating for exactly 2 weeks today. Yesterday I transferred most of the bottles to the refridgerator, and today I opened and drank one. It was in fact carbonated (though slightly flat, compared to commercial beers), didn't have much of a odor, but did have a very strong sour, green-apple/acetaldehyde taste to it. Otherwise the beer is fine. Drinking it right now.
Was it sour like lactic acid (yogurt) or acetic acid (vinegar)? If so, check your sanitation procedures. Or was the sour really just a part of the green apple? Edit: if it has some vinegar component, then it may be from oxidation of alcohol too, so watch your oxygen/air uptake during bottling.
(1) Since the beer is already bottled, is it too late to remove this off-flavor by more aging, or can that only be done by conditioning the beer in a secondary fermenter?
Yes, it may be too late. The little bit of yeast in the bottles may be able to help, but it would take much longer than the full load in a secondary fermenter. Bulk aging works better.
(2) Since most of the beer is now in the refridgerator, are their yeast now dormant, such that putting them back in a room temp storage cabinet won't result in them carbonating/aging further?
Not only dormant but sedimented on the bottom. Moving bottles back to warm may allow the yeast to continue to work, with a gentle over-turning of the bottles to stir up the sediment. But perhaps they really are done and all the sugar is gone. Perhaps you just didn't add enough (you didn't say). The standard volume measures are 0.75C corn sugar dissolved in 1 pint water and added to 5G beer. Does the beer also taste too sweet/sugary?
(3) What can I do in the future in general to prevent such a sour off-flavor?
Acetaldehyde or green apples can be left behind by incomplete fermentation. Allow the fermentation to fully complete by leaving on the yeast longer or making sure you pitch a healthy active yeast slurry. The smack packs or tubes are really not enough even for 5 G, but we get away with it if they're fresh and the wort has plenty of oxygen added through pouring, shaking, or pure O2 addition. Consider making a yeast starter (search for tips). Easiest for next time is pouring the wort into the fermenter through a strainer to remove hops and aerate at the same time, then shaking the sealed fermenter vigorously to dissolve the headspace air, do that 5 times for 1 minute each, opening to get fresh air in each time. That's easier for me in a carboy with a good cap than a bucket with a loose lid.
Sounds like your thinking is already on the right track. Give the beer another 1-3 weeks without drinking it. If it's still green-apple then just think of it as a dark Bud (known for its acetaldehyde) and try again. Hope that helps; let us know how the next one works out.