One problem with the whole configuration and installation process is that Henrik Johnson refuses to use autoconf and instead uses a big, ugly Perl script. Not only that, but I think parts of it are broken and there are lots of hard-coded directories. I've started going through it line by line and I'm re-writing it as best I can.
Ultimately, however, I suspect a few of us need to get together, hog-tie Henrik and lay into his back with a stiff elbow until he says, "Uncle! I mean, autoconf! autoconf!".