I'm really impressed by the sum of work you placed in this package which is absolutely needed in PEAR.
Unfortunately, I could not vote +1 with conditions as you are too far away from PEAR coding standards and this conditions would be a total restructuring of the package.
It's too much confused.
One very important point you are missing is the basic rule in PEAR: any package must function based on a unique include_path: the pear base dir.
You are not allowed to "arrange" it, or only in very peculiar customizing oriented cases.
Also, the file structure must reflect the class inheritance, so any developer can go to the code in a glance.
So, I'm very sorry to ask you to reconsider your proposal (withdraw, re-factor and re-propose), it's not meaning the code is bad but not acceptable in PEAR as it is. Please don't take it as a reject, my goal here is to ensure your package will start its life in PEAR in a right way and not as a lame duck.