Seems that you need do make clean after you have changed your configure
parameters. I am not sure what is your current state, but I would
suggest "back on trees" approach and start from scratch here. Download
current devel-msts-unified_makefiles branch from CVS, do the configure
with all suggested parameters. Run make (report result) and finally make
install. 
If you want to see the installation result, you can add
--with-root-dir=SOME_DIRECTORY_WITH_ABS_PATH and check that directory
after make install. If everything is correct then you can either copy
all files/directories to / or run configure with same parameters except
--with-root-dir and simply do make install again.

I downloaded the latest version using:
cvs -z3 -d:pserver:anonymous@pdfedit.cvs.sourceforge.net:/cvsroot/pdfedit \
co -r devel-msts-unified_makefiles -d pdfedit-test pdfedit

then ran autoconf -v and got:
configure.in:4: error: Autoconf version 2.61 or higher is required

so then I checked autoconf --version and got:
autoconf (GNU Autoconf) 2.60

so I searched the fink package list but it seems 2.60 is the latest fink has. So I guess I have to build autoconf from source without finks help! I'm giving up for tonight. That's a fight for another day.

James.