I have some questions about notation.
Generally, if two chords appear in the left hand, each with three notes, and there is a slur mark over the top two notes, does this mean all three notes of the first chord are slurred into the second chord, or just the top notes?
I would say generally yes, but not necessarily always.
Wouldn't it be rare to find situations where the same finger doesn't jump from one key to another, making a true slur without pedal impossible?
If you mean that for a true slur you would need to have six fingers (or borrow one from the other hand) or else be lucky that one finger can slide off a black key onto a white one, yes. But sometimes it suffices to give the effect of all being slurred even though you're actually only slurring one or two. There are no hard and fast rules. Also, just because it doesn't tell you to use the pedal, it doesn't necessarily mean you shouldn't.
Regarding a pair of two-note intervals--is slurring both notes assumed if the fingerings allow it, such as 1-3, 2-4?
Probably, but it depends on context. I'm not sure what you mean by "if fingerings allow it". If there are fingerings printed, and they make slurring easy, then it probably does want to be slurred, because that is why that particular fingering will have been recommended. But remember that in general fingerings are not provided, and even if they are, they are just a suggestion, and something different may work better for you.
In a specific instance, I saw G-B-F followed by C-E in the bass clef, with a slur over the F and E. There were no fingerings included, so I used 5-4-1 for the chord and 2-3 for the interval--correct?
Yes, that's fine. But think of it more as being suitable
rather than correct
. In general there is no such thing as "incorrect" fingering. Use what you like, provided it works for you and doesn't get in the way of the result sounding the way you think it should.