At the beginning of the movie, for example during the transitions between Frodo&Gandalf and Bilbo writing, the first shots that are after the transitions are in a different colour than the ones that follow them.
Also, during the movie, there are some shots with no video (the screen is black), but the audio is synchronized and goes properly during the black shots.
Now about the edit itself:
The backstory is not very well presented to the newcomer audience: for example, during the first shot of Mordor (Gollum tortured/Nazgul coming out of Minas Morgul), the audience doesn't know what this is all about (the only clue that there is somehing about the Ring is the Eye of Sauron seen by Gandalf when he tries to take it). In the original EE, we know about the Ring and Gollum.
In addition, the changes to the presentation of the backstory are not really more faithful to the book. Everybody knew about the battle of the Last Alliance; it wasn't included in the Scroll of Isildur. Also, the newcomer audience wouldn't know what that is about.
My suggestion: restore more scenes from the prologue with the Gandalf narration from BFME and add them before the "This is the One Ring" line told by Gandalf to Frodo. Also, in the original movie there are two scenes of Gollum being tortured: one before the Scroll of Isildur scene and one in a flashback later (Gandalf telling about it to Frodo). You should merge them and add the resultant scene where the second one is in the original.
What is very faithful to the book is the removal of the Saruman scenes, which is done very masterfully.
In the FOTR Book-Cut Version 1 thread, you said that you put "17 Years Later" when the Nazgul first comes to the Shire. This isn't present in the current version.
Why did you use another title card? I didn't understand that.
Also, I didn't understand the sounds that are heard during the final shot ("The Journey Continues on Disk 2"). I think that it is the Sea.
Anyway, this is my review. I hope it will be useful.