I got it figured out. I had to set the newly added quest aliases to Optional and Allow Dismissed so it would allow the main quest controlling the follower to initialize.

I have a custom follower that only has "Skyrim.esm" as a dependent. It works fine when importing her into Enderal. This is the original mod: https://www.nexusmods.com/skyrim/mods/83958 The problem arises when I tried to use the patched version I created to address bug with the original mod: https://...