After much stripping and rebuilding of various parts of the engine over a few days we are now running on two cylinders again, the culprit turned out to be a pin in the injector pump that had not been knocked into its groove and was allowing part of the piston to rotate and not draw any fuel through. It’s back together now and running like a different engine, all the vibration has gone from the boat when it’s running, the exhaust note is much quieter and the throttle response is immediate. If I put it in reverse while still tied to a pontoon now we’d probably tear the cleats off.