Hi Jason,
If you take a look at the validator in the clump finder that is using the cython `gravitational_binding_energy` function, you'll see that there is already an option to use particles in the gravitational binding energy calculation. See the `_gravitationally_bound` function in `yt/analysis_modules/level_sets/clump_validators.py`.
When you create your master clump, all you need to do is set `use_particles=True` when you add the `gravitationally_bound` validator to the master clump. In fact, the example in the yt docs does this:
Hope that helps, let us know if you need any additional advice.
-Nathan