> For some reason, the linker *does* generate manifest files for all the
.pyds when I try it out. Should that worry me? When I delete them, it
still can import them just fine.

Hm, works for me. I am using MS SDK v6.1 and PCbuild/build.bat.

> This is not true. For MSVC9SP (VS2008) Microsoft decided that by 
default, it will still compile against the original CRT

You're right, there are defines for that:
http://msdn.microsoft.com/en-us/library/cc664727.aspx

While that won't load a 2nd copy of the CRT into memory, the embedded
manifests of site-packages still have the same problem as the .pyd files
now. So if this gets accepted, reverting the patch of Issue 2563 should
be considered.