Heh... Yojimbo is, IMO, one of the most complex parts of the game... check out this FAQ on how to make him do Zanamato (which will kill any enemy): http://db.gamefaqs.com/console/ps2/f..._x_yojimbo.txt

If you haven't been doing what the FAQ says, then I suggest you try either A) paying him all your money/millions or B) start to follow the FAQ and hope you can get his motivation high enough.