Consider a re-write and use the old site as a feature specification
Surprisingly, no one even mentioned this, as far as I can see, but there is another alternative: give up on the code and just use the functionality of the site itself as a new feature set specification (i.e., the first one ever for this project) and then re-build the site, based on those features, with an established framework (such as Symfony, Laravel, or Drupal).
Yes, there are those who would cringe at the evil word re-write ... but there are cases when this is actually a better way to go, and you hinted at some reasons:
- you're fairly new to PHP development, yourself
- you will probably be better off starting out with something clean instead of the pure crap code you've inherited
- in the final analysis, most users don't give a damn about the source code, and if it looks like it "works" to them, they may look at you like you're crazy if you try to tell them something is dreadfully wrong
- you will have more fun and live a longer life if you pick up the practices of source revision control and database design within a unified framework that looks like someone actually cared enough to have their name attached to it
Sure, everyone in this position has had to work with code like this before, but sometimes enough is enough and it's better to scrap the spaghetti and start with a fresh plate.
If you read Joel's article on why it's bad to do a re-write, you will notice almost none of the circumstances he cites apply to you here.