Is that the model with the strange firing order (points close at the same time....)? That aside, if the atom modules are connected to the coils the same way as the original factory connections, it seems to me it could work. Presumably, that would be through the charge coil.
Maybe the other option is to find a mag plate for a traditional magneto from the '50s or '60s, and use that with a fresh set of under flywheel coils.