First of all, I cannot wait until this comes out. I first saw a very badly abuse version when I was perhaps a sophomore in high school, and still was astounded. Then I was incredibly fortunate to see it again many years later, after I had graduated from college, in a restored grand old theater with an actual pipe organ and live orchestra, and it was even more amazing.
Second, I know it's very dangerous to pop in and make undocumented statements ..., but I could swear I heard a report not too long ago (on NPR perhaps) about the score for this restoration. I seem to recall discussion of them crafting new music for the added "lost" segment using themes from the original score for inspiration.
I'll see if I can find any documentary reference to support this. It is admittedly a somewhat dim recollection.
*EDIT*
First, apologies: I clearly had it a little wrong. I believe this is the story I was thinking of:
http://www.wbur.org/2010/04/23/alloy-metropolis
According to this, the Alloy Orchestra, which had created an original score for the film "more than a decade ago", have gone back and created an extended original score to account for the new material.
I've seen several other comments suggesting that this is the score played with the restored film as it plays around the country this year (I do not know from personal experience, as I have not yet had the pleasure). Here is one such reference (about halfway down the page):
http://twitchfilm.net/news/2010/07/sfsff-2010-lineup-preview.php
But, if you look a couple paragraphs above the heading "Back in the Studio" on the NPR piece, it seems to say that the original score will be on the DVD release (though no mention of what's being done with the new footage), though the Alloy Orchestra is hoping to be included in a "special features" edition.
Hope that helps.