I'm not quite sure that I am understanding what your goals are, but it sounds interesting. I'm no audio engineer, but I do goof around in Audacity and VinylStudio from time to time when cleaning up flaws in my record and CD library. I'd like some software that can merge two or more copies of identical vinyl pressings as a snap/crackle/pop noise removal technique. There is an existing patent on this concept, it is about 15 years old or more IIRC. However I don't know if there is any TooT-type audio merging software that is commercially available. Being able to separately save the sounds removed from a process similar to this is what I think you are trying to accomplish. Perfect alignment of waveforms I think is key to everything, I see you mention on a per-sample or 1ms basis. I wonder if zero-crossings are sufficient alignment points?