Hi @headswillroll1789, glad you liked my template.
The changes you’re after are not small, especially number two. If I knew a fix for number two, I would have implemented it. But the current situation is a consequence of how the persistent field feature works, namely that it persists the content in persistent fields, and then appends changes below existing content.
Without grouping the annotations by color under headings, this isn’t too much of an issue, but’s it’s quite annoying with the duplicated headings. I try to minimize updates/re-imports for this reason.
However, I’m going to try to implement a workaround for this soon.
As for the order of the annotations and comments, the comment you linked to was not regarding a current version of the template. There’s another comment here with code that moves the comments after the annotations: Zotero Integration – Import Templates? - #224 by untidytexts
That one is more recent, but still not current, as I’ve made lost of improvements since. But it might give you some idea of what needs to be done. I don’t have time to make these changes for you at the moment.