When draining oil via the oil drain plug will all the oil in the engine including the crankcase sump drain be drained? Or will some oil remain in the engine?
As far as I know if there is oil in the sump it will not drain. I think there will always be a little oil in the sump. Make sure you let it idle upright for a couple minutes before draining. I believe the manual say's to start with 4 quarts and add till full. I start with 4 1/2 quarts, ride till reaching operating temps (15 to 25 miles depending on outside temps) and add from there.
It will remain in the sump. It is important to warm the bike up to operating temp, then let idle WHILE UPRIGHT for a couple minutes before shutting down, then change oil. If you want to drain the sump, most (not all) oil will come out if you pull the crank position sensor. There is also a case plug, but the case is thin and I don't recommend pulling it.
It's not a concern. Warm and idle as mentioned, drain what comes out and refill.
Yes, you'll still have oil in the sump, as well as the cam compartment, oil filter and oil passages throughout the entire motor.
I let mine drain over night in hopes of getting as much out as possible.
Only the pan drains. To drain the sump you would need to pull the crank sensor. And to drain the cam chest, you'll need to pull the cover.
As for letting them sit over night, its not needed. Just drain the oil warm and when the stream of oil turns to drips, close it up.
I just like to make sure I get as much out as possible, makes me feel better. I also poke a couple holes in the filter and let it drain overnight as well. That way the filter is not hot and doesn't make as big of a mess. I know it doesn't drain the sump or the cam chest.