If you get the new  fdftkv5.tar.gz  from adobe's site (per the link above), you'll get some totally new spacing and capitalization of files.  To make the current 4.3.1 configure, you need to do a few things.

untar fdftkv5.tar.gz into /usr/local
cd /usr/local
#for ease of use
ln -s FDFToolkit\ for\ UNIX fdf

cd fdf
ln -s Headers\ And\ Libraries HeadersAndLibraries

#may need to modify the following for your OS
ln -s LINUX linux
cd linux/C
ln -s LIBFDFTK.SO libfdftk.so

cd ..
cd ..
ln -s Headers headers
cd headers
ln -s FDFTK.H fdftk.h

And that should get you going... and to whoever is maintaining the configure script, please be aware there are changes in the FDF Toolkit.