I highly doubt that Kuja was originally female in the Japanese version. He is clearly male, even the FMV's showed that. He has no boobage at all.
Also, I give you this: http://www.tagalog-dictionary.com/cgi-bin/search.pl?s=kuya
KUYA means "older brother" in Filipino. KUJA might be pronounced "Koo-jah" with a harsh "j", or "Koo-yah" with a soft "j", like the Filipino word. I think this is pretty obvious that Kuja was always Zidane's "older brother".
Also, I give you this: http://www.tagalog-dictionary.com/cgi-bin/search.pl?s=kuya
KUYA means "older brother" in Filipino. KUJA might be pronounced "Koo-jah" with a harsh "j", or "Koo-yah" with a soft "j", like the Filipino word. I think this is pretty obvious that Kuja was always Zidane's "older brother".