First of all, let me say thank you for the time you have taken to create this. I was one of the fortunate few to get a copy of the MKV you put together last year and it is easily the best home version of this film I have ever seen. I have a 3D movie projector and 150 inch screen and watching this film with the 3-D the way it was intended is truly a dream.
I echo the sentiments that were written in the other posts in that when the 3-D works in your version, it really works amazingly. The unfortunate side effect of course is what you have already noted in that the scenes where it is 2-D there is sometimes pretty bad ghosting or blur and it sometimes takes away from the effect or makes the film difficult to watch. Not your fault of course.
What surprises me is that given that both eye prints are out there that others have not tried to make their own side-by-side version using the same two prints that you have. I wish I knew more about the technology to help you create this. My thoughts would be to take the version you have with the awesome 3-D effects and then also find a way to go 2d for the segments of time where the ghosting was occurring – in other words, just overlay the same for both eyes which I would hope would take away the ghosting. Without a full length version of the other eye that’s the best we can do.
To me, this is a holy Grail of a home 3-D viewing experience, and I can’t believe that Paramount or Warner Bros. have not done something to make this title happen. I would pay premium amounts of money to own it. Your version shows how amazing this can look.