Some of this is not so hard. I think you need to use japanese version as start and edit text in there. This way you will have all scenes that has been deleted, almost every language (there are most of world languages are stored in font file and you could use them).
#1 - I would like to add in a couple of the dummied enemies into random encounters. Does someone have a list of the battle formations, the list of which formations are on which maps (and the enemy hex #s)? I know where the enemy data is stored already.
Probably the hardest part, because we don't know how enemy's encounters stored.
#2 - Do you think it would be possible to add in the deleted 'Sophia painting' scene into the actual game at some point?
If you use japanese version as start point thia problem automaticly solved.
#3 - Has anyone made a text table/extraction from the japanese version?
Nope, only english. But it not so hard to expand it to japanese version.
#4 - Once I extract the text, how can I reinstert it? (and how would I reinstert it if I add in more text than originally, since the translation will take up more space that was allocated in the english version - will it have any effect on the placement of text from other areas if I expand one area?)
English editor automaticly recreate file after save. Though you has restriction on file size. (size of file must not exceed the original sector's size)
#5 - After extracting the movies (japanese) and subtitling them, how can I replace them back into the ISO?
Some people already create util for subtitling xenogears movie. (
http://www.sadnescity.it) They translate xenogears from english to italian.