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I was also an Emacs user for a very long time, and only started using Org mode (relatively) recently. I can heartily recommend it - it has become my almost exclusive use of Emacs. I have a few pointers to the resources that helped me get started in the Org section of my old config file at https://github.com/zzamboni/dot-emacs/blob/master/init.org#org-mode. You can also see there a good selection of configuration options and packages that I found useful.
Note that I said my "old config". A few months ago. I decided to try Doom Emacs. Over a couple of days, I ported most of the important bits of my decades-old, hand-maintained config, and in the process realized I could get rid of a lot of scaffolding (like the whole package-management bits in your config) by virtue of Doom's existing mechanisms, and also I could omit a lot of the configuration because Doom includes decent defaults for many things. I have not regretted moving to Doom. You can find my new config at https://github.com/zzamboni/dot-doom/blob/master/doom.org.
One particular thing I can suggest for equations is dynamic latex equation previews, which toggles TeX source when the cursor is on an equation but when it goes out of it it toggles a rendered preview. See this and this, adapted from this).
One package that was helpful for note-taking was org-autolist. I took all my notes as outlines and that made it faster.
Org-sidebar would have made navigating class notes even easier.
Because I started my program a while ago (and I'm now well past the coursework phase), there were some packages that hadn't yet been developed (or were in their infancy) but that I absolutely wish I'd had at the beginning of my program for taking notes on courses and readings: org-noter, org-roam, org-ref, and org-roam-bibtex. Since you're just starting out in a program, you might take a look at these. (I plan to implement these fully into my workflow once I get a bit more time.)
Backup: backup-each-save, saveplace, and configuring auto-save. Plus whatever automatic off-site backup works for you. (I've been saved more than few times by automatic backups!)
Version control with git and magit. I use git even for non-software projects, like writing. For writing projects where you don't want to interrupt your focus/workflow to commit, you might find git-auto-commit-mode helpful.
Writing: writeroom-mode, wc-goal-mode, flyspell, and adding some nice aesthetic options. I created some tips for writing in org-mode here.
PDFs: pdf-tools is helpful (but a new maintainer is being sought and so how much you can depend on that long-term isn't clear to me yet).
Org-modules and add-ons: org-pomodoro (just noticed in searching that there's a "plus" version but I haven't tried it), org-inlinetask, org-wc, among others.
I also second the suggestion of another poster on counsel, swiper, ivy, etc. (I love this suite and the various add-ons). I'd add ivy-bibtex.