cygwin ended up being the solution here for me:
diff -N -x .svn -rup ./original_trunk ./new_trunk > patch.diff
cd to ./original_trunk
patch -p0 < ../patch.diff
original trunk should now have the changes from new trunk.
Hardest part about this is getting the diff and patch utilities installed in cygwin. I installed the patch utility using apt-cyg and diff I found in the cygwin installer.