The Ultima Weapon can be gained after you've come back from Terra and there is no more Shimmering Island. Take a chocobo to the spot where the portal to Terra used to be and use a Dead Pepper to fish up the weapon.

You have to get to Hades in under 12 hours in order to get Excalibur II.

The Ragnarok is a Chocograph treasure item, and I seem to remember finding it in a crack on a mountain on an island somewhere. Whatever the case, I'm fairly certain it's in a crack (the kind for which you use a Dead Pepper to explore). I'm sure the EyesonFF main site has this info.