Here is where everything fell apart, and the only reason I'm uploading this at this point is for my own records. The following were planned story lines that just never happened, or were dropped entirely to get the ending over with.
-Restoring Rarity
-Restoring Rainbow Dash
-Restoring Fluttershy
-The Diamond Dog Tunnels
-Recruiting Princess Celestia
-Return to Manehattan
-Recruiting Discord and Alicia
-Silver not getting his horn back
-Finding the Elements of Harmony
-A trip to Evodia
-A meeting with Novaria