IMHO the main problem with using PEAR packages without installing PEAR is paths.
Many package files have include and require lines that depend on the files being where they look for them. eg.
You can either hack all such occurences in all the PEAR files you're using to make sure the paths are correct.
Or you can do ini_set in the "top" files eg.
(colon for *nix - semi-colon for Win)
'include_path', ini_get('include_path') . ":" .
$_SERVER['DOCUMENT_ROOT'] . "/path_to/PEAR/");