I was thinking that maybe the whispers were in each person's head and that they were a result of maybe Jacob reading their minds. Jacob draws from someone's memory and presents an image known to that person in order to convey a msg to them. The sudden appearance and disappearance supports the idea that they're nothing more than images... images that can be shared by more than one person obviously since Jack was able to see Harper.
I think it was Jacob giving Juliette instructions but stating that it is Ben who wants the deed done because it has to be someone who Juliette would listen to. We've no evidence that Ben has psychic abilities so how could Harper have been instructed to find Juliette (at a specific location and time in the pouring rain in the middle of the jungle) while being confined by Locke. The whispers seem to occur just before people or things appear so, IMO, it must be Jacob getting stuff done.