What is the mileage of the car and what makes you suspect it is the engine rather than transmission (not saying it isn't just tying to understand more).
Is it a metallic knocking or more a buzzing vibration?
If you can still drive the car get it to the revs/speed where it's making the noise and without moving the throttle change down a gear. Does the noise change? Then accelerate and see if it comes back at the same road speed but with higher revs.
Are you in the UK and, if so, is it with a garage/dealer who understand the S&S?
We are in the UK and the car has done about 5500 miles. A while since I have driven it now but it felt like the noise was coming from the front and just 'felt' as if it was engine rather than transmission. More revs than road speed for one thing.
Agreed that I need to drive again and put a very analytical view to it.
The garage is a Morgan dealer and service centre but I suspect that their technicians are more used to higher tech engines. I'm not knocking them. They had the balls to ring up and say that they don't know what it was and to discuss what we do next because it could start getting expensive. Hence my search for a common problem that may simplify matters.
However nothing obvious is surfacing. Not the first or last person to have an awkward noise that is difficult to diagnose I'm sure.
After all this I will probably find that it is a loose seat runner or something inane as per Karlosfandango's theory above.