Get it under revision control.
Decide on naming conventions and file/directory structure.
Make sure you have decent tools/IDE.
Set up a separate development/testing environment if you haven't already
THEN ...
Unfortunately, you'll need to sift through all those 1, 2, 3 files and determine which ones are in use, and which can be disposed of. No other way besides a brute force grind through, file by file.
Even though I have an RCS in place, I still often move what I think are unused scripts to a hidden location, say .mausoleum and then have the RCS ignore that location. Nice to be able to take a peek locally without going back to the repo.
Separate HTML and PHP to the greatest extent possible. I cannot stress this enough! If this is done in each file, fine. Just so long as you have separate chunks of PHP and HTML. Of course, HTML will be peppered with echos here and there, but try to have all tests, switches, everything else moved out of the HTML block and into the PHP block. This alone can be HUGE when it comes to getting things sorted out.
If the code is primarily procedural -- I assume in your case it is -- it's probably best to do some clean up first, before doing any serious refactoring or refactoring into classes.
As you find files/scripts that can logically be combined, do so. (I've seen projects -- probably not unlike yours -- where the total number of surviving files is about 1/4 of what we started with).
Once you've gone this far, then you can begin a proper refactoring or refactoring into classes.
Bonne chance!
