Could please post
1) full output of the command (sorry for asking again, but I would like to know when happens in your case when USE_PYTHONCONFIG=y is defined)
cd $NWCHEM_TOP/src
make link
(or make FC=... link)
2) output of the command python-config --libs
PS The recipe I gave you works for me on Debian ... I would like to understand what is causing your failure.