After troubleshooting some problems with deployment of the SCCM Client to Windows 7, 8.1 and 10 devices, the manual installation worked however when your try to connect the client to a site it fails with "Configuration Manager did not find a site to manage this client." In this environment the SCCM infrastructure had been rebuilt twice previously, as this was a test setup to simulate a real deployment of SCCM 2012 R2.
The problem was caused by two things, the first is that I had not get the default Site for the Boundary Group the problematic client was in. To check or resolve this click Administration/Hierarchy Configuration/Boundary Groups. Right click on the Boundary Group and select Properties.
Click the Reference tab, click the option Use this boundary group for site assignment, select the correct site from the drop down. Then click the Add button and select the corresponding site server.
This only corrected some of the problems, newly built clients that had not had any visibility of the old installation of SCCM were fine, they could resolve the Site Code without problem. However old clients that were previously managed by the old SCCM installation still failed. This was because the old installation of SCCM was configured to deploy the client via GPO's. In the GPO's the Site Code had been statically configured, this is a setting that is tattooed onto the client machines Registry. Even after the GPO was removed from the computer the SMS Site Code is still in the registry, in my example this Site Code no longer exists, hence it causes the problem. To resolve this open the Registry on the problematic installation and browse to Local Machine\Software\Microsoft\SMS\Mobile Client.
Inside this folder there was an entry "GPRequestedSiteAssignmentCode", in this instance this was set to the old Site Code. I deleted the entire entry and it resolved the problem.
