ArcGIS uses a different version of the msvc libraries than what you're including, so once they try to load there's a version conflict when it tries to import your local ones. I'd recommend getting rid of the manifest altogether.
If you're using a setup.py to build, the thing I do is patch \PythonInstall\Lib\distutils\msvc9compiler.py and locate the following lines:
And just comment them all out.
# embed the manifest
# XXX - this is somewhat fragile - if mt.exe fails, distutils
# will still consider the DLL up-to-date, but it will not have a
# manifest. Maybe we should link to a temp file? OTOH, that
# implies a build environment error that shouldn't go undetected.
mfinfo = self.manifest_get_embed_info(target_desc, ld_args)
if mfinfo is not None:
mffilename, mfid = mfinfo
out_arg = '-outputresource:%s;%s' % (output_filename, mfid)
self.spawn(['mt.exe', '-nologo', '-manifest',
except DistutilsExecError, msg: