I'll number based on your post's paragraphs with a zero index :)
1. Safari is my daily driver, so I'd have to trawl other people's dotfiles/bootstrap scripts for evidence anyone's handling FF in a smart way. But, this might still help: Apple recently changed Safari extensions to be an adjunct to native apps. Before they made this change, I had a section of my bootstrap that used the `open` command to launch the Safari extension page for each extension I used, which made it pretty trivial to click install on each tab.
Another thing you might find tractable is looking for FF config/state files that you can back up and restore (narrowly). This is easier to play with if you have a 2nd system as I mentioned. I figured out, for example, how to restore my macOS Terminal.app windows from my previous install with all of my scrollback history.
2. These are rough, but you're already on the right track. It sucks, so maybe bitch at Apple about it--more voices might move the needle here. I have 3 basic approaches: find a defaults (and, rarely, another command) that does the same thing; figure out which plist file is implicated and diff it before/after changes until I figure out how to force the right change (broadly, I find it better to try preference edits with all involved apps closed); AppleScript it. I have applescripts in my bootstrap for stuff like setting my Finder preferences and enabling specific Safari extensions (now that they're bundled with .apps). If you haven't already tried it, UIElementInspector makes it much more plausible to actually write an AppleScript that has to do UI manipulation.
3. No direct comment on nvram as I've never fiddled with it, though I noticed it does have an option for outputting the current settings and a flag for setting them from a file. For defaults, I'm not sure there's anything better than just not doing it unless you add it to your script. (This is where I was wondering about whether there's a good way to diff my delta against my setup script...)
4. Too vague for me to give a good answer. If you can't find a way to set these from the CLI or hacking around with plists, I'm not sure anything shy of AppleScript will help.
5. What do you mean by wireless configs? Passwords and network names? I pull mine in through iCloud keychain and don't otherwise sweat these.
All my Firefox plugins and their config (I guess this is technically data)
All the settings I've changed though the control panel (I can't figure out every file that changes when I make a change).
Any time I've changed a setting with nvram or defaults
Most of the settings of the default apple apps.
My wireless configs
This is always the part I get stuck on.