This could be a good frame of reference - http://www.brentonfilm.com/articles/nosferatu-the-ultimate-blu-ray-and-dvd-guide

Be careful to avoid using anything from Kino’s blu-ray. Somehow they managed to delete every 8th frame.

I wish you the best of luck. I too once tried to sync up Gillian Anderson’s recreation of the Hans Erdmann score to the latest restoration but found I couldn’t sync it. It could be that her recreation had to be condensed a bit to fit onto one audio CD, or maybe she based her recreation on a shorter, earlier restoration of the movie. What I had considered doing was a hybrid of hers and Berndt Heller’s recreation, but couldn’t make the time for it. However you do it, I would love to see the results! 😉