> It may actually be enough to just place the 
Microsoft.VC90.CRT.manifest file into the Python folder (the one with 
python.exe and the CRT DLLs).

I concur with what Christoph says, that is how the embedded 
installation works. However, the .pyd files are not in the Python main 
folder. And therefore they shouldn't have a manifest for the runtimes 
(because it will look in the current folder relative to the DLL/pyd), 
because then the runtimes of the main python.exe will be used (which 
can then be in the same folder as the 'embedded' MSVCR location).