^ The pieces added to TPM since 1999 (extended pod race for example) are in the 3D. The cropping is closer to the 1999 version, for home video the movie was significantly chopped. and factor in this:

http://moviesblog.mtv.com/2012/01/27/star-wars-phantom-menace-3d-preview/

So when you start a conversion, do you start from the beginning or the middle or the end?
We worked in an odd order, because with Episode I, we were also doing a restoration. One of the first questions that my Associate VFX Supervisor, Dorne Huebler, and I started asking, was that if we were going to take this movie and cut it up into 2,000 separate pieces, we had an opportunity to upgrade what those 2,000 separate pieces are. It seemed like we had a perfect opportunity to go back and create a cleaner, sharper and purer version of the movie.

In fact, the window was closing on that; these archive tapes don’t last forever and they haven’t been meticulously catalogued and archived because no one thought that was really the master of the film, so it wasn’t clear that we were going to be able to find all of them.

Where did you find them?
They were in a variety of places. It was some work to find them and we found about 98 percent of them.