Well I have it working finally. Microsoft had a great article on removing and reinstalling IIS which worked great except for one small caveat The arrticle is Q320202 but the caveat is that when it talks about uninstalling the Client access Roles and says you can do it from the Add and Remove programs Well it does not seem to remove everything. I did this twice and had the same problem Since I knew my problem was because of Webconfig files being empty. I would check them and they still were empty.
So how did I fix it. I used the Command line listed under step 3 plus since I was having a problem with UM installing (the service would not start) I inluded it in the uninstall Even though add and remove programs/change exchange still showed it as being uninstalled. When I ran the command below it found the UM role and uninstalled it plus all files and the services.
exsetup.exe /mode:uninstall /roles:CA, UM
This even stated it was removing files and appears to have done so because all the actual files were removed that were related to UM. I Then Rebooted the system and reinstalled both roles through cmd line. it works great now.
Hope this helps someone out.