But worked around the bundle loading issues by creating a separate :shoulda bundle in Gemfile referencing the rails3 branch. Then removed any requires for shoulda and put the Bundler.require(:shoulda) into test/helper after all the rails environment has been required.
Rudimentary tests are working. I've yet to try custom macros and functional tests.
git submodule add http://github.com/thoughtbot/shoulda.git vendor/plugins/shoulda
cd vendor/plugins/shoulda
git checkout rails3