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A and B are not sonically identical - for something that is sensitive to phase they are cheese and chalk. The time domain is where the action is, not the frequency domain. But you have brought up a key point - it is incredibly hard to perfectly synchronise two waveforms to truly extract what the difference is at a certain point - quite a bit harder than what you and Dennis are suggesting. I've managed to fool myself a couple of times by having less than 100% synch, thought I had something real, but it evaporated when I had a rethink.
DiffMaker lives in a dream world, with the numbers it comes up with - Dennis has remarkable faith in it, I must say .
To see my comments and conclude I have remarkable faith in it is some high distortion indeed.
There are people who can use matlab to do each of Diffmakers steps without the various hangups you run into. I don't know enough about matlab or the math to do that. (might could learn the math if I applied myself, I just haven't the knowledge in that area of math off the top of my head) The principal is sound, the software is buggy and error prone. When it works, it really has worked. There is other software you can get most of the way there without writing it up in mathlab procedures. Again the principals are sound and work.
So it isn't easy, but in principal doable and can be done. Diffmaker attempted to make it possible for anyone to do it.
The primary difference in 8 and 9 is about 27 ppm in timing rate. Using 16 million pt FFT's and other processing to speed up or slow down you can match peaks with high accuracy and adjust timing to confirm you have it synched to high enough accuracy to get below -100 db on nulls. Adjust levels as well and you have it. It isn't magic. Just science.