Go to Edit -> Preferences -> Add-ons -> Install and select the zip file you downloaded
In the search box, type in 'ffxiv' until the addon 'Object: FFXIV MMD Tools Helper' shows up and check the checkbox
Once you see "FFXIV MMD", you'll know it is installed correctly. All of the tools are located here.
Not needed (but recommended)
FFXIV Export to Blender Stuff:
Anamnesis - Used for finding out the character data in FFXIV leveraging the .chara file. This addon is now integrated with it to make it faster and easier to use!
FFXIV TexTools Used for exporting the character data into .FBX format - Video Tutorial - watch the first 7 minutes
XAT FFXIV Animation Toolkit - Standalone tool for manipulating animations and skeletons in Final Fantasy XIV. Needed to play any custom animation .pap files created & exported out of blender
FFXIV MekTools Blender Addon for Blender to fix inside-out alpha (if you're not using this tool to import). Also, it has a pretty good skin shader, but I haven't gotten all the controls to work properly to be honest. This addon is now integrated with it to make it faster and easier to use!
UuuNyaa's MMD Tools Helper Blender Addon addon for MMD Tools for Blender, a bunch of useful tools for animating MMD Models (including lighting presets, material presets, physics tools etc...)
Animation Retargeting Addon for Blender - Needed to copy animations from one model to another model (such as a MMD model to a FFXIV Model) since they have different bone names and bone structures. Used in conjunction with the XAT addon to play MMD Animations in FFXIV. This addon is now integrated with it to make it faster and easier to use!
Auto-Rig Pro - A paid application that does what Animation Retargeting Addon does, but apparently is faster and easier to use. I don't know, I never tried it, but the more experienced FFXIV XAT animators swear by it.
Gravity Collider Bone Physics Addon - I haven't tried it, but its a free and easy way to add skirt and hair physics (if you're sticking simply in Blender)
MMD Animation in Blender Stuff
The original MMD model (.pmx file) that the VMD animation files were based on (useful for animation scaling reasons)