I think the solution to the problem you are facing is going to be two parts. The first thing is allowing you to select php type of files from the browse server interface. The next thing is setting up the user files path to point to the root of your site. Once this is done you should be able to browse to files on your server to link to them.
To get it so that you can select php file types you will need to configure settings in two places. The first is in the HTMLEditor/fckconfig.js file, you need to add php to the FCKConfig.LinkUploadAllowedExtensions:
FCKConfig.LinkUploadAllowedExtensions = ".(7z|aiff|asf|avi|bmp|csv|doc|fla|flv|gif|gz|gzip |jpeg|jpg|mid|mov|mp3|mp4|mpc|mpeg|mpg|ods|odt|pdf |png|ppt|pxd|qt|ram|rar|rm|rmi|rmvb|rtf|sdc|sitd|s wf|sxc|sxw|tar|tgz|tif|tiff|txt|vsd|wav|wma|wmv|xl s|xml|zip|php)$" ;
Along with adding it to the allowed types you will also need to remove it from the banned types. This is in the KFM configuration.php file that is located at HTMLEditor > editor > plugins > kfm > configuration.php.
In here you need to find the variable name $kfm_banned_extensions around line 128. In here you need to remove the php entry so that it looks like this:
$kfm_banned_extensions = array('asp','cfm','cgi','php3','php4','php5','phtm','pl','sh','shtm','shtml');
The next part is to set the user files path correctly to point at your root directory. To alter this setting go into HTMLEditor > editor > filemanager > connectors > php > config.php. In here look on line 42 for the $Config['UserFilesPath'] setting. You should try setting this to be blank like this:
$Config['UserFilesPath'] = '';
On the next line this value is updated again, don't worry about making edits to that one.
Give this a try and let us know how it works for you.