Looks pretty good. Nice adaptation of an existing package for PHP5 features. Couple of suggestions before it gets my full vote.
1.) Code needs to be run through phpcs.
2.) There are a lot of spelling errors in the API documentation. Spelling should be checked and sentences should start with correct case. Additionally, some documentation actually seems incorrect. I suggest reviewing all the API documentation to make sure it still makes sense based on the updates you've made.
3.) @access tags are only needed for PHP4 and should be removed.
4.) Text box graphics in the header can probably be removed. They'll look funny unless you use a fixed-width font. Extra author info doesn't need to duplicate @author tags.
5.) Exception classes should go in separate files.
6.) User_Exception should be UserException unless it goes in a sub-directory.
7.) Docs reference singleton() method, but method is getInstance().
8.) It's not a singleton as you create multiple objects. It's a Multiton (http://en.wikipedia.org/wiki/Multiton_pattern)