To echo what people have said:
1) It's the entire one way direction.
2) You can choose to, say, apply it to a single sector so that, in your case you could have it apply to JFK-NRT only so that if that failed to clear you wouldn't waste an entire GUC on just NRT to SIN.
3) I've had GRU-ATL-SEA clear on GRU-ATL but waitlist on ATL-SEA and then had ATL-SEA clear separately.
4) I've currently got a GUC applied to just LAX-SYD on a SEA-LAX-SYD ticket so that either I keep the GUC or I get to sleep on the way to SYD. (I'm assuming SEA-LAX will upgrade, if not, then I can cope on a short flight).
The thing I'm not sure is if say, JFK-NRT clears then can you call up ask that NRT-SIN is applied against the GUC as well.
1) As I said earlier, it's not the entire direction if there's a broken fare. It depends on the fare component. Also, at least for SWUs, you could een have a stopover and use a single GUC per direction if the fare allows stopovers versus being constructed with three one way fares.
Yes you can waitist only the most significant segment and when it clears add the other segments, still using a single GUC for the entire direction.