Regarding the later partitions, if you want to access them, download Unleash-X and use it's file manager, as it accesses all partitions (plus it can view .txt files, which can sometimes be useful).
Regarding the .xbe, sorry I have no idea, but if I were you I'd delete and re-install Morrowind GOTY, then follow the tutorial at
http://forums.xbox-scene.com/index.php?showtopic=480384then install the mod, but don't copy over the .xbe from the mod package, use the one you've just edited yourself.
Good luck, and let us know how you get on.