Help me finding a way to create my Academic Workflow

I am planning to transit to Obsidian from OneNote, but I am getting a hard time on trying to figure out a Workflow for my research and PhD work.
Myself: A life science PhD student and Researcher.

Reference management system: Readcube Paper. This is the issue. Most of the workflow are based on Zotero as reference management system.
Why Readcube? I like the web-based app, and it has a good PDF viewer.

I do all the highlighting and annotation in reference manager.

Furthermore, I also use readwise for getting notes from other web-based article including RSS and transferring to obsidian

Planning to use obsidian for a) Note-taking, mostly from Research article read and annotated on my reference management system & RSS reader.
B) Analysing and making notes and generating ideas: Connecting notes using linking and generating ideas
C) Using notes and as original reference to write research papers, articles, and thesis.

Issue:

  1. How to get annotated notes from reference manager, keeping the link between notes and reference intact. (How can I take advantage of a web-based reference manager ?)

  2. How to get bibliography in to obsidian and use it to cite the notes and article it has created? I can use citation plugin but as per latest update the Windows based Readcube application does not generate an automated .bib file. I can manually take a bib file, but whenever I update my library, I will have to again generate a new bibliography file.

  3. Using PC-based app, I have all the PDF files of my library. How can I take the annotated article PDF files in obsidian and linked it with the bib file and annotation and notes from that article which i have taken from web-based app?(The PDF downloaded by Readcube does not have/show highlights and annotation which I have done in the reference manager itself.)