[queries numbered in brackets]
Not sure how you imagine it but
"The software would be a combination of Evernote + a todo list + related file explorer" sounds promising

Tagging and filtering to show the relevant info sounds good.
[1] With hierarchical tagging? (I've never used Evernote online, dont know what it has/does).
I tend to be a bit of a chaotic worker, but this seems like it would cover all the things I need to do. I work with many files, get a lot of feedback with requests for modifications. Working with information from other people, I have many queries too. So the communication aspect would be very important to me. Priority ordering of queries in both directions. Ability to sort according to ones I have to answer, & ones they have to answer (that should be easy with tags).
So, for me, the inbox -- as in
"capture informal requests, ideas and suggestions" -- would be ongoing throughout a project.
ToDo would also therefore be an evolving process as project continues.
In a bigger project, reviews would be done at different times/phases.
I'm sure you've thought of this, but above was just to point out that 0, 1, 2 & 3 could all be happening at around the same time on an ongoing basis (or e.g. within the same day).
[2] Which shouldnt be a problem (?)
[3] Re the file explorer - do you mean you would create your own file explorer within the app? (Easy access to same file or folder in default file manager would be important.)