I happened across this tool to help you create configs, it looks pretty good, easier than piecing together all the parameters separately: https://www.digitalocean.com/community/tools/nginx

Seems like it has directions for certbot and generating dhparams, etc. as well.

I would approach it this way:

1. Learn to configure and install Jellyfin the way you like it. You sound like you have a good start on that. JF handles metadata for you, and you can also manually match items if/when it matches up. The only extra plugins I install are some of the ones for extra metadata providers and TMDB box sets.
2. Setup Jackett with the qB search so you can run manual searches for stuff against your indexers.
3. If you want to use docker, learn docker. There’s a million tutorials around. You can use Docker Desktop on Windows if you want a GUI to help you out. Since docker on Windows runs on WSL2, it’s a good opportunity to mess around with Linux if you aren’t familiar.

From there you can work your way up to full automation and such if you like. I don’t think it’s necessary for most people.

As for data layout, just make some folders like movies, tv, music, etc, and lay out stuff in there logically. If you have a fancy storage setup, you might do separate shares for them, whatever works for you. Some people like to link from their “download” folder into their actual media folder to keep things clean. You can do hard and soft links on Windows with NTFS, but it’s kind of a pain.

Mullvad doesn’t have port forwarding, so that’s going to be a factor.

I think what you have is fine, and wouldn’t worry about it too much.

That said, I run unbound with pi-hole, directing the dns queries through a wireguard tunnel. It’s a bit slower, but I do like having my own recursive DNS, especially with news that more and more services are implementing DNS level blocking.