Mission 45 is annoying me now, it's the last one of the challenges I need to beat but he just kills everyone with one hit with that Screech(?) move

Sounds like an Ochu?

attempted the final boss again, got to the second part and got the HP down to 1.5 million but I took too long fighting the boss so my party leader was Doom'd

Are you using Light as a RAV to stagger each of the legs? Light's RAV AI has a tendency to prioritize Elemental Strikes over normal spells, thus she has to approach the legs to hit them.

Being near the legs, there's a 50% chance that your melee strikers will suffer a double hit instead of a normal hit from the stomp. That can do up to 23K damage with no damage reduction. even 25% damage reduction still puts it at 18K damage, which is her exact max HP. 

Sazh is a lot better since he's ranged and has a high amount of HP.

Also, I've found it's a lot better to use Fang as a SYN and put Vanille and Light as SAB. I don't even bother with buffs at the start of the fight, I just start with Auto-Bravery for Fang and Auto-Haste/Auto-Faith for Light and Vanille. That's enough to take down the legs in less than a minute. When the Adamantoises are falling down, I switch to Fang SYN and use Faithra/Bravera/Haste on all three, while Light and Vanille are busy putting Deshell, Deprotect and Imperil (Imperil is a must, you won't drive up the chain link to 999% otherwise). After that, it's just a matter of tearing up a new one to the adamantoises/tortoises. 

Edit - My bad, she has 20K HP at maximum CS evolution. 25% damage reduction should be enough to get her safe through a double hit. 

well, you can easilly prevent that to happen if you change to Sen/Sen/Sen right before the Stomp. (4k..?) if i had to rate the Characters in Battle, i'd go with the following:

Vanille: 10/10 (She IS a Beast, and i manage to deal 999.999 Damage w/her once the enemy is staggered., i killed Long Gui when he felt down first)

Lightning: 9,8/10 (Sadly, she is missing some good skills in some Class-Roles, but she is the best ravager, imo)

Fang: 9,5/10 (Great Commander, but not as useful in other Roles as Light)

Hope: 9,4/10 (Greatly Doing his Job as Syn/Rav, and yes, he hasnt as much life points as the others, but i dont care.)

Snow: 8/10 (The BEST Sentinel available, he can eat damage as it would be nothing. Long Gui's Stomp deal's 100-200 Damage with total defense. but he lacks some Strength and Magic, so the others are a bit more useful in other Roles)

Sazh: 6,5/10 (He's the only one with offensive Syn Spells, but once that Changes, he's Useless, because his stats does suck.)

How much magic do you have in order to pull that off? I have 3K magic and even to 999% staggered Adamantoises, I only do 200K tops o.O

tried to switch to Commander (Com/Com/Com) before the Death Skill Hit's?

i have around 3k with Vanille too, and after insane Buffing/Debuffing, i am dealing 999.999. (okay, not everytime, sometimes it is just 800.000-900.000 :((( )

During the animation of Death? Nope haven't tried that. Does that make any hit that connects during that animation, a 999.999 strike? o.o

well yes, you have the 2,5x Damage Bonus from the Commander Role, and additional 1,2x of everyone else who is, when you change before the Death-Animation show's the Number.

this, connected w/ all useful Buffs and Debuffs will lead to insane Damage.

I'll try that then xD But how did you took down the legs of the Long Gui before hand? Since you're using Vanille as the party leader, you don't have access to Highwind, which is the fastest way to take them down.