Okay so this is something I'm working on now to try and properly and completely isolate the whispers, it will take a while though. A long while. Basically the easiest way to isolate vocals from a track is to invert the off-vocal of a track and mix it with the original version. The two instrumentals cancel, leaving the vocals behind. However, S* hasn't given us an instrumental or off-vocal of Prologue III which makes this a little more trickier. (And I don't think he'll give us one if we ask him)
The way I think this can be resolved, and what I'm currently working on, is to listen to the audio behind the vocals, find an exact replica of it in the track, and cut that clean audio into the space where the vocals are. It seems far fetched but the audio underneath the vocals is repetetive in parts and could quite simply just be pasted over the track. If I (or anyone else who wants to try) can do this correctly (and more importantly REALLY BLOODY PRECISELY), we should get an off-vocal track that can be used to isolate the vocals.
Obviously this doesn't have to be done for the whole track, only the parts we're unsure of or don't know, but the important part of this is that the two tracks must sync up exactly on the sample level to get best results.
If anyone knows the time-code of a lyric we don't know, tell me and I'll try and do this for it. :)