Sorry to resurrect, but after following all the steps here I now have PW working fine in its own IIS site. However i actually need PW working as a subdirectory of a root site. Currently the homepage is fine, but anything else is getting handled like a 404 of the root site. Cant get to the admin or anything. Any ideas? 
Main Site - example.com  
Desired PW Site - example.com/pw 
Thanks!