Hi there, this SOUNDS to be a cool project !

I honestly don't know if it's in project goals, but some time ago I discovered a very cool lib called Aurio that "focuses on audio processing, analysis, media synchronization and media retrieval and implements various audio fingerprinting methods".

As this video demonstrates, those algorithms can align (through its GUI called AudioAlign) fingerprinted audios between many tracks.

The drawback is that it has been developed in C# for .NET (Windows-only), so it would be really great to establish some kind of collaboration between projects in order to (finally) obtain a platform-indipendent open source multitrack synchronizer.

Hope that inspires.