Andrew, have you ever done a Frequency Analysis of it? I'm just suspicious about why you had to remove those gaps that were originally there. Either the person didn't extract it correctly (didn't have his offset set correctly in EAC perhaps?) or perhaps the original source was mp3.
I'm a Mac person, so I'm not familiar with all that EAC does (I didn't know it removed gaps between tracks), but I did want to get in here and let you get some feedback.
Also, going shn to flac is fine. Five wrote a tutorial on how to do this without actually going to wav using foobar2000
here, but you needed to go to wav because of the gaps.
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