Hey @PR2ndbrain, and welcome to the forum!
You write this, but from your subsequent points under “what I have done so far”, it sounds like you’ve got a solid, functional system already. The questions you have seem to be fairly minor issues:
That appears to be the local graph (or an equivalent zoomed-in view of the global graph) of your Zotero Integration template. You can tell by the grey color that the code variables are not actual notes, but links that could be realized.
This is merely a consequence of the fact that the template contains links that will be made when you import an item from Zotero as a literature note. This includes links to: images, each author of an item, and a link to the collection names the item belongs in.
To eliminate these links from your graph, add this under Filters in the graph options (upper right corner of the Graph):
-path:"Your/Template/Path", with your actual template path.
In addition, if you are not interested in creating author notes and collection notes, then you can remove the square brackets that surround these in the info callout.
My template is sort of geared towards Journal articles, I must admit. For example, I don’t distinguish between creator types. There are some examples in this thread of more dynamic processing of creators and such, as well as importing the item type and storing that in the frontmatter. You could add those parts to the template to accommodate other sources (I will do this in a future updated version).
Zotero can handle many types of sources, so this should be a viable option. It also added annotation support for webpages and Epubs in the latest Zotero 7 betas.
I use Readwise to store and import newspaper articles, tweets and such, so I have a template for that which is sort of similar to this one, in that it also formats the annotations as a list. However, Readwise is not free. There is also Omnivore, which is free and open source, but I can’t comment on that since I haven’t tried it.
You are meant to fill these in yourself in Obsidian after importing (given that you want such a workflow). The code fields there are cursor placeholders that you can jump to, in order to quickly add the information. You need the templater plugin for this, which is very widely used. I have a hotkey set up so I just need to press ctrl + J to jump to the next cursor location.