All of the characters should have Strength, Defense, Magic Defense, Accuracy, and Agility at 255 and Luck at 80 or higher. Stoneproof/Ribbon, Auto-Haste, Auto-Protect, and Auto-Phoenix are also very useful, if not necessary. Dark Yojimbo always ambushes you in the first battle, even if you have Initiative, but you can still get a turn before him by using First Strike weapons. Kozuka and Daigoro target only one character, so they are not very dangerous, but Wakizashi deals about 25,000 to the entire party. It can, however, be reduced under 9,999 by using Protect, Cheer and Defense+??%, so Break HP Limit is not necessary. Yojimbo's Overdrive - Zanmato - kills everyone, ignoring Auto-Life. The only way to survive is to call an Aeon. Interestingly, against a shielded aeon with Protect, his Zanmato will only deal around 50,000 damage.
As any other enemy, he can be killed instantly by Yojimbo's Zanmato attack, but it's extremely hard to get it five times in a row, so a weak party stands little chance against him.