I am in possession of the disc images of unreal 2 the awakening, gog does not have the game listed so the install script can not pull it like it is told to. Is the disc images compatible for the gog version?
No, the gog versin will want the gog installer.
You are best off mounting the disk images, possibly using something along the lines of CDemu to make them truly appear as if they were cds.
Then install from whatever install.exe (or setup.exe, or similar) is found in the main cd (Click the plus at the left top → Intall a windows game from an executable → enter relevant details, and the path to the previously mentioned executable)