$_SERVER['SCRIPT_NAME'] = /wp-admin/admin.php

the output url is:

http://domain.com/wp-admin/phpuploader/ajaxuploaderresource.php?type=script

Which is not correct. The correct path is doamin.com/wp-content/mu-plugins/phpuploader 

I do have things working on my production server, but it is not a full proof solution, I will test any other methods you would like or I canlook at this more when I have resolved some other issues my host has caused with this migration/upgrade they have done to me hosting.

Thanks,

Jesse