I just thought I'd put a simple post on this subject as in my searches to find away to do this I never found anything conclusive and there appeared be some confusion as how to do this.
Obviously all missions and collections need to be completed including the new DLC chapters (sequences 12 and 13).
The 3 missions exclusive to the black edition are required.
The uplay mission for the Auditore crypt is also required. (I found this out after being stuck on 99.29 for a while). As may the other rewards - better to do them as anyone with the game can get them (PS3, XBOX 360 or PC).
Secret areas within crypts do not contribute, dying or killing civilians (I've done this accidentally now and then) do not inhibit synchronisation.