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2014-02-12, 20:03
Have you maybe applied partition mod along the way? That also happend to me, but on a stock rom. I even prefer it that way, because I like to have all of my big files on external sd (like obb/data game files), so that way I don't have to use FolderMount in order to redirect files loading from internal to external sd card. Can't tell if it's a bug or a mod feature, but it came to me as a bonus 
Regarding recovery, are you sure you have TWRP? Because GG's version have CWM recovery. So if you really have TWRP maybe the version you have installed is not fully comaptible with V3. It should handle the "new way of memory management" in 1.0.4, because you still have phone storage as before, but it's only merged with data partition. That doesn't change anything on recovery level and everything should be as before.
Regarding recovery, are you sure you have TWRP? Because GG's version have CWM recovery. So if you really have TWRP maybe the version you have installed is not fully comaptible with V3. It should handle the "new way of memory management" in 1.0.4, because you still have phone storage as before, but it's only merged with data partition. That doesn't change anything on recovery level and everything should be as before.
If I helped you, clicking "Thank You" button will be enough.