Greetings,

Thanks for the questions! Sorry that some of the wording caused some confusion, so let me clear it up.

1) Can we use a single piece of music from the game and use that as our music for the entire video? That is to say, if we record in locations in the Central Shroud, and have several different scenes (recorded separately), are we allowed to mute the sound in those scenes and then use the Central Shroud theme from beginning to end (with no gaps) as a single piece of music for the video?
Yes, you can.

2) Can we pick a piece of music from another part of the game and use it in our video, or are we restricted to the music from the area where we record the footage? i.e. Say we film in Mor Dhona, but want to use the Limsa Lominsa theme music for the video as a whole. Is this acceptable?
Yes, you can. You are not limited to using music that only appears in that area of the game.

3) If we use music at all, must we only use the music that plays during the actual gameplay footage we record? i.e. if you go to Gridania, there is a theme that plays in the background as you run around. If we were to mute that sound and substitute another piece of music from the game for the whole footage, would that be acceptable? Or must we only use the music playing in the background at the time the footage was recorded?
No, it does not need to be music only from that scene for you to use it.

Any of the music that is used in-game, or songs that appear on the Before Meteor soundtrack, or even the sound effects in the fan kit, is fine to use in your video over any FFXIV game footage.