You may need to download the newest version of IFOedit (v. 95) from Doom9.org. I really can't recall how reliable .94 was for stripping angles, it's been so long. (I was a beta tester for Derrow, so I've been using the .95 version for some time. Even with version .95, though, there are times when the angle option is greyed out... but it just may work here.)
If DVD2ONE recognizes that there's different angles, then it should be able to isolate the one you're looking for, though... but if you want to restructure the DVD so that the menu's still there -- and then use DVD2ONE on a "full disk" copy -- then I'd say it's an IFOedit thing.
Another thing that may be confusing IFOedit is that the menus themselves have several variances: You may get the asteroid chase lead-in, or the Obi-Wan/Boba Fett fight, OR the chase through the power cuplink. Either way, this disk's a challenge.
But, yeah, download version .95 and see what it says when you run your original files through the "VOB Extras" option.
ALSO: On this disk, KEEP all the subtitle files. That's the only way I could get my forced subs to work. I'm not sure why; but when I backed up Windtalkers, the forced subs were in the French folder! So -- at the very least -- test the disk before burning if you take out any subs... you'll save yourself a coaster.