There is no more Modules/Makefile, use toplevel Makefile.

sysconfig.py

@@ -142,7 +142,7 @@ def get_config_h_filename():
 def get_makefile_filename():
     """Return full pathname of installed Makefile from the Python build."""
     if python_build:
-        return './Modules/Makefile'
+        return './Makefile'
     lib_dir = get_python_lib(plat_specific=1, standard_lib=1)
     return os.path.join(lib_dir, "config", "Makefile")