incantation to build vim in such a way that pyflakes works

gistfile1.bash

# NOTE the /Modules/

./configure --prefix=/vol1/home/brentp/installed/ \
     --with-python-config-dir=/vol1/home/brentp/src/python/Python-2.7.2/Modules/ \
     --enable-pythoninterp=yes --with-features=huge 

still couldn't get pyflakes to work the last time I checked, I remembered it was something about vim not built with python support?

yes, that's exactly what this is supposed to address. You have to tell it the python-config-dir (not sure if the other stuff is required).
If you do | grep -i python you can make sure the ./configure worked.

This config-dir works for me with the default python-dev install on Ubuntu:

http://stackoverflow.com/a/5293524

now I'm doing something like this

CFLAGS="-I /software/common/python/2.7.5/include/python2.7/" ./configure --prefix=/software/common/vim/7.3/ --with-python-config-dir=/software/common/python/2.7.5/lib/python2.7/config --enable-pythoninterp=yes

where Python.h is in the -I directory and config.c is in the config directory.