It's not as bad as that, Psi. You can save between fights, just don't reset.
Don't use Stoneproof, use Ribbon instead, since it actually protects against Daigoro. Auto-Haste and Auto-Phoenix are also highly recommended. Have as many Celestial Weapons as you can (Masamune, Nirvana and Onion Knight work best, since they aren't weakened by your character being in critical). Spam Quick Hit and Aim (iirc, he has insane evasion). The only reason to perma-kill Yojimbo (five wins without resetting) is to fight Penance, so you should max your stats before trying it. Get a ton of Ribbon armour first, though, so you can experiment with different configurations of abilities (Auto-Haste, Phoenix, Protect, Potion, BHPL, etc.) without having to collect 99 Dark Matters each time.