If you already have experience with Nvivo just stick with it! If you work within a university you probably have access to a license for free, if not there are ways to get it if budgeting is priority. Nvivo/MaxQDA/Lookback best handle the coding/theming process to analyse qualitative data. Word is great to handle multi-authoring/editing/commenting/revisioning. Mendeley is great to organise your literature, highlighting PDFs and simplifying the referencing process. But there is a reason why certain software specialises to do certain things. I know you feel the need to do everything in one place - I have that too. You are pushing the limits of Obsidian and while on the one hand I do really hope you manage to achieve what you need, it's worth thinking whether you really need investing time to set this up, or whether this is just the procrastinator inside you tricking into thinking you need to do this? I am saying this because I have spent countless hours doing things like these rather than doing the actual work :P One straightforward example is: how do you assign to the same sentence two different codes?
This process was originally developed for psychology research by Virginia Braun and Victoria Clarke.
In my experience, Obsidian is great for taking/organising notes, but it will not handle the analysis. There are various approaches to conducting thematic analysis, but the most common form follows a six-step process: Familiarisation. My two cents as a qualitative researcher who has worked in academia and is now a consultant.
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