The Masamune is in the last dungeon. The Ultima Weapon, or "Atma sword" if you like, is at the end of Whisperwind Cove, the Soul of Chaos dungeon that's near the Ice Cave, in that maze of rivers.

Edit: Dear Mr. Sixteen Hundred,

I don't know what kind of sick pleasure you get out of consistently posting immediately before I do and thereby negating my very existence, but I must say that it is totally sexy in any case.

Carry on,
The Kish