Fight the monsters around Wutai and get the Enemy Skill "Magic Hammer" from them (you'll need to Manipulate them to cast it on you). It makes your character absorb 100 MP from the targeted enemy. Then have Yuffie use Magic Hammer on Godo ten times until he's out of MP. That means he won't be able to heal himself or use some of his spells. After that, just fight him and defeat him. Alternatively, if it's late in the game, you may use KotR to defeat him (my friend actually did that), although I think that's an overkill.