Have you drunk whiskey?
You're correct that this asks if you have ever drunk whiskey in your life, but I think it would be more idiomatic to add the word before to the end of the sentence:
Have you drunk whiskey before?
Have you been drinking whiskey?
This does indeed ask if they have drunk it recently, though it might have other more subtle implications. One possible scenario:
Person A: I used to drink beer most of the time, but lately I've switched to harder liquors.
Person B: Have you been drinking whiskey?
This means have you acquired the habit of drinking whiskey recently, not have you drunk it today. Another case:
(A parent sees a half-empty whiskey bottle and a tipsy child)
Parent: Have you been drinking whiskey?(!?)
In this case they are clearly inquiring if the drinking has taken place in recent hours. So depending upon context, either meaning can be appropriate.
This tree has stood here for 400 years.
I don't know that has stood here implies a permanent action; it's more the 400 years that does that. (That is, you feel a sense of Well this has been so for 400 years, how likely is it to change now? that really has nothing to do with the has stood here). All that has stood here for [x] years implies is that this was the case for the prior 400 years; there is no implication of what may or may not happen in the future. Consider:
This tree has stood here for 400 years, and now you're going to chop it down?
This peace has reigned for 400 years, and today we celebrate that it may continue for many more!
Depending on context, what you refer to may or may not be implied to continue, but nothing is implied just by the has [x].
This man has been standing here for 15 minutes.
This is the same as number 3; all it says is that for the preceding 15 minutes the man was standing there, it makes no implications about the future. The reason you see a difference between this and #3 is that you used 400 years in one example and 15 minutes in another; that's where the expected level of permanence is coming from.