I'll get to this when I finally do a playthrough, but here are some suggestions:
From the CT Prerelease:
* Track 14 -> for the 1005 AD Cathedral, Fiona's Shrine, and Vision Serpent's Hall?
* Keeper's Dome -> can probably replace one or two instances of Black Dream.
* Battle 1 Rough Version -> Reptite Timeline battle theme?
* Tyrano Lair -> Alternate boss battle theme like in PG?
From CT PSX/DS:
* Scattering Blossoms -> replaces Memories of Green?
* One Sunny Day When We Met -> replaces Guardia Millennial Fair?
From RD/CC:
* Frozen Flame -> Frozen Flame appearance in Unto the Breach, and maybe even throughout all the FF nightmares for a continuous nightmarish atmosphere (I don't know, maybe it'd be too long though).
From CC:
* A Narrow Space Between Dimensions -> End of Time theme, since we use Brink of Time in Chronopolis?
* Singing Emotions -> I'm not sure where this could go, but this would be a great "nostalgic situation" theme and it's one of the CC tracks that fits the most with CT due to the absence of guitar.
* Navel of the World -> Prehistory overworld theme?
From Treasure Conflix:
* Unused 5 -> Porre march?
These are just rough ideas; some tracks like Frozen Flame, etc. are clearly more important than the others and we probably won't do everything in this post (finding the right instruments is totally tedious and boring).