Sam,
A rod, at least to my ear, wouldn't be described as a 'deep' knock while a main bearing would. If it's a rod bearing, you should be able to get it to bang at will.
Revving the engine up and gradually letting the throttle fall will let the rods float for a second and should make any offending rod knock. If the exact cylinder can be found, pulling the plug can sometimes make it knock a bit more steady and pronounced as there is not explosion in that cylinder.
Don't rule out goofy things like a water pump or a generator that's gone south. Use a length of rubber heater hose as a stethoscope to pinpoint the origin of the noise.
Stuart
