I would think you can use virtually any Bonnie engine from all unit construction years, like BSA, Triumph rarley changed anything major on their bikes during model upgrades they were generally minor cosmetic changes. If your a bit more adventurous you could try slotting a BSA engine in the frame, Remember BSA and Triumph were at the time virtually one, Rocket 3 is a BSA name for the Triumph Trident, albeit with minor differences, both I'm sure shared the same frame, I would not be suprised if an A65 engine would slot straight into a Bonnie frame, it may even be possible to fit a Trident T150 (I fink) or a rocket 3 engine in.
Ian