First step of course would be to put it under version control. This way at least you can go back to the original working version. Secondly it might be a good idea to overwrite the include, require, etc functions to, for example, write the filename of the file that's being included to some log file, this way you can find out which files are actually being included (thus hopefully ruling out a lot of the index2.php, index3.php, etc.
To find out, if necessary, if some classes are used and some aren't, you can use get_declared_classes in conjuction with get_defined_vars and gettype to see which types are being instantiated.
As for issue 4 and 5, those are probably a bit harder to solve, but this should get you started hopefully.
