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.

I've installed gtk2/pygtk2 but the build script says that it can't find it.

You probably haven't installed the development versions of those packages, so the required header files aren't present. Development packages usually have names ending in -dev, such as python-gtk2-dev on Debian.

I get a long error message ending with KeyError: 'shlib'.

See the Ubuntu Installation Notes.

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.

On OS X, OOF2 crashes as soon as I try to load an image.

The ImageMagick libraries have probably not been built properly. Use the Console app (in Applications/Utilities) and look for a report called "Python_[something]" in the "DIAGNOSTIC AND USAGE INFORMATION" section. If the report contains something like this:

Thread 3 Crashed:
0   libMagickCore.4.dylib         	0x0000000102b5d12c gomp_resolve_num_threads + 28