Blind or Pain on ST-ATK, make sure you either have Alert on or one person dead, as the second Ruby will get a Back Attack on you, and will normally use Breath ASAP. Use Doomtrain on the Rubies as well, as they generally get Sleeped. --- Humanity's one redeeming virtue is the ability to corrupt anything.
Note that properly junctioned as defined by my posts typically means:
HP: Full-Life/Regen/Quake (whatever puts it close to 9,999) Str: Ultima/Meteor (whatever puts it as close as possible to 255) Mag: Meteor/Pain (doesn't matter since magic isn't great in this game) Vit: Meltdown Spr: Reflect Speed: Triple/Stop/Haste
Ruby Dragons: Try to have the Meltdown spell junctioned to your Vitality. That will decrease the damage done by their Breath attack. Honestly, they're not very hard once you take that precaution. Protect reduces damage from Breath if I'm not mistaken. Aside from that, you could kill one party member to prevent them from using Breath at all, but if you're trying to maintain 0 KOs for your characters, it's not the best idea. You can also limit spam them and kill them off quickly, though it should only take one Duel from a properly junctioned Zell.
Bahamut: Just about the same as any other boss, but try to keep your HP high when Mega Flare is coming. Aura spells instead of critical HP will likely be the better course of action, though you could just start the battle with a critical Zell and end it in one Duel like anything else in the game.
Ultima Weapon: Light Pillar is really the only thing that can kill you if you're properly junctioned, but he can be killed before he gets a chance to use it. One character to draw Eden, one character to cast Aura, then a Duel from Zell will finish it even without putting Ulty into Vit 0 with either a Meltdown or Doomtrain. If your reaction time is a bit slow and you need the Vit 0 status to kill him, go for it.
Just keep in mind that if you kill Ultima Weapon, the fixed encounters in the DSRC are gone forever. If this isn't your "perfect" file, then you can go ahead and do whatever you like. If this is your perfect file, you may be better off keeping him alive and just getting the Eden card and Eden GF on the fourth disc from the CC group and Tiamat respectively. Ultima Weapon offers absolutely nothing unique once you take those into account.
The only things one might say are unique about him is the "challenge" of facing him and his existence in the first place, both of which are also gone forever without sufficient reward if you defeat him. To preserve the only unique thing about him, you could just save before facing him and reload after you beat him. The fixed encounters are much more useful than the reward you do get from Ultima Weapon. The only reward you get without taking the card and GF into account are the 100 Ultima Stones, which pale in comparison to the fast and infinite supply of Curse Spikes for Dark Matter that also refine into 100 Ultima.
In fact, if you ever decide you have enough free time in your life that you want to max luck, it's literally hundreds of hours faster to completely restart the game to bring back Ultima Weapon than it is to try and max luck with him gone. That doesn't even take into account the other items worth farming from the fixed encounters. --- I am a man. The CIA is just a cover.