The swig files won't compile.

You're probably using the wrong version of swig. OOF2 requires version 1.1 build 883. You'll have to delete everything from the SRC/SWIG directory, and replace it with a fresh copy from the oof2 distribution (or just delete your entire oof2 directory and start over). Then build and install OOF2 with one command, like this:

python setup.py build --skip-swig install --prefix=prefix

I get lots of messages like this during compilation:
Warning(124): Specifying the language name in %typemap is deprecated - use #ifdef SWIG<LANG> instead.

You're using the wrong version of swig. See above.

coordcmodule.C won't compile, indicated by a long string of error messages beginning with SRC/SWIG/common/coordcmodule.C:2776: error: cannot allocate an object of abstract type 'Position'.

You're still using the wrong version of swig. See above.

OOF2 crashes on startup with an error like this:
ImportError: Failure linking new module:
/usr/local/lib/python2.4/site-packages/oof2/SWIG/image/oofimagecmodule.so:
Symbol not found: __ZTIN6Magick9ExceptionE

Your ImageMagick installation is incomplete or inconsistent. Perhaps you have two versions installed, and oof2 is using header files from one and linking to another. Perhaps your ImageMagick library was compiled with a different C++ compiler than the one you're currently using.

My stiffness matrix is not square.

You probably haven't accounted for the third dimension properly. You need either to specify that a field is in-plane, or to activate a plane-flux equation.