As someone who platted FFX back in the day - and I never want to do that again, let me tell you - I'd hope I'm...somewhat knowledgeable. xD
But you're not going to want to see this: ultimately it boils down to luck. There are elements that will contribute towards the probability of Yojimbo using Zanmato (which you seem to be aware of) but it is still down to random chance as to whether or not he'll actually use it. The only advice I can give you, since you're aware of the factors that will maximise your chances, is to keep trying if you're really determined to go down that route. You can only influence the odds so much, and then you just have to cross your fingers and pray. You're not doing anything wrong - it's the game that doesn't want to cut you a break. I'd recommend reading
this guide for a more in-depth guide as to how the game calculates whether Zanmato is used or not if you haven't already.
Honestly it would be faster to just max out stats, because you could be trying for hundreds of hours if you intend to do EVERY superboss that way...especially if you count the Monster Arena creations, of which there are many, and many don't actually require maxxed out stats to beat, so you could do them as you go. It'll go by faster than repeatedly trying and failing superbosses if you split tasks up - run Don Tonberry a few times for AP, then run something else for Spheres, go catch some more monsters, etc. It really doesn't take very long at all to max out stats - if you want to do everything you need to capture 10 of every monster for Nemesis anyway, so you'll have access to Species/Arena Conquest monsters that will give you the tools for the job. Sure, it'll still take you around 20-30 hours with a plan, but you could spend the same 20-30 hours trying again and again for Zanmato and never get it...relying on RNG is worse than grinding, I think. But then, that's just me.
You don't actually need to max EVERY stat either - Strength, Defense, Magic Defense, and MAYBE Agility (don't quote me on that; I can't remember off the top of my head if it's necessary) at 255 are all you need. Accuracy and Evasion have a more complicated relationship that mean you won't need to max both, and you can get by with pretty low Luck levels if you use Aim or Rikku's mixes to compensate for that and don't mind the occasional miss - you need 85 to hit Penance's arms IIRC (which are the only things you absolutely NEED to hit every time if you want to survive) and 5 uses of Aim gets you 50...and really you should be using Hyper Mighty G or Ultra NulAll - or both - for superboss battles anyway. You don't need to use Clear Spheres, and you don't need TOO many of each type of stat sphere to get there.
Do you have Wakka's Attack Reels and Celestial Weapon? You will chew through pretty much everything with that once you're set up - that's a quick win on everything except Dark Anima and Penance...and the Dark Magus Sisters if you try and do all three of them at once, but nobody who doesn't have something to prove does that. Anima and the Magus Sisters will do crazy amounts of damage the higher Yuna's stats get, too - Oblivion and Delta Attack are much quicker and easier to use than Zanmato, and just as lethal for anything that isn't a higher-tier Dark Aeon or Original Creation. Honestly, of all the Dark Aeons, only Bahamut and Anima will give you grief if you max out your stats, and you don't even need max stats for the weaker ones like Valefor, Ifrit, and Ixion. But you can easily get Auron's, Rikku's, and Yuna's Celestial Weapons, saving you the pain of minigames (because the Catcher Chocobo is poison, Blitzball is FAR worse than stat maxxing ever was, and dodging 200 lightning strikes in a row...well...yeah) and they can carry you through quite easily. It's not as bad as it sounds, and the best thing about it is that you WILL win if you do it - no relying on unfair RNG mechanics involved.
I speak as someone who hates RNG mechanics and never got a Zanmato despite trying the same things you did - despite people on the internet screaming that it was foolproof, 100% guaranteed, etc - so yeah, feel free to ignore me if you want. But I can tell you that you're doing everything you possibly can, and that the thing you see as a pain isn't THAT much of a pain if you split up the various tasks you're going to have to do anyway if you want to tackle Nemesis with it.