Alright... i sort of agree with your theory BUT... not all of it...
I think Sephiroth actually did all that on his own... not JENOVA... theres no reason for JENOVA to take his form... i think every since before in Nibelhiem Sephiroth became influenced by JENOVA and did whatever she said, since she was his "Mother" or whatever... BUT Cloud killed Sephiroth before he tried to leave and JENOVAs head was lost as well...
Now, if you notice... the Sephiroth with no legs... hes in the area with the WEAPONs if i remember correctly... IMO he was being re made in that substance similar to how the WEAPONs are being made... of course it takes a long time... years to be exact... so hes actually been there the whole time... but he projects himself to other places like what he did in Shinra Headquarters... thats how he can fly all over the place and everything... and disappear and stuff....
Now in Advent Children... the Brothers Kadaj, Loz and Yazoo... they supposedly have the head of JENOVA... and they are planning to have another reunion... which makes me think.. that Sephiroth with no legs... I think he is now complete and the only thing needed now is... the reunion...
Thats what i think... if anyone thinks otherwise tell me.. ^_~
