After googling everywhere the last 48 hours to find out why my server suddenly stopped working, and finally, finding the answer myself, I decided to post it up here for anyone else who is googling a whole weekend away on something so trivial.
Loaded everything on nginx, LEMP working perfectly, but then I tried to do some SSL modifications and in the middle of everything it stopped working.
I've completely removed everything but the necessary lines in sites-available/www (my version of sites-available/default) and checked that nginx.conf is correctly formatted without double includes that I've seen mentioned in other places.
It appears the a file sneaked into my configurations and messed everything up. It's an autosave file called nginx.conf.save which gets in the way of the original nginx.conf configuration and causes a Page not found error.
Now back to getting PHP working with SSL... happy times!