Are you planning to have your software analyze the tracks at several points during the recording, in order to make sure that things continue to remain in sync? I don't know whether clock drift between any two particular sources remains a constant or not, but if not, then it would seem that intermediate points would have to be established. I imagine that there would have to be a millisecond inserted here or there in order to compensate for the drift, which hopefully can be done in a completely silent manner.
This would make dealing with my four track set up a lot easier, because I could just load them into Audacity, run this program, and then take the two tracks back into Soundforge, which is my personally preferred post production program. Looking forward to seeing and/or testing your software.
Wow, if only I had known that I could have gotten a college degree in taping.