Hi singinmgr, welcome to Outdoorking.
There is an abbreviated version of the Honda workshop manual available as a free download, here:
http://www.honda-engines-eu.com/documents/10912/31965/1531/209cf374-f289-4c75-9fea-6ecb5353e447However I do not think this will help you with your present problem. I suggest that you should begin by removing the blade plate complete with blades from underneath your mower. Be sure to disconnect the spark plug lead first, then tip the mower toward the oil filler, not toward the carburetor, to get access to the underside. With the blade plate removed, put the mower back on its wheels and reconnect the spark plug lead. See if the grinding noise still occurs when the engine is run without the blade plate.
Usually when you run over something with a mower it is the blade plate and blades that are damaged, though in severe cases the crankshaft may be bent as well. However crankshafts usually bend at the lower main bearing, which does not cause major distortion inside the crankcase. A bent blade plate may not make contact with the mower base unless the engine is running.
If the noise disappears when you remove the blade plate, the crankshaft may still be bent. You can check this by rotating the engine slowly, with spark plug lead disconnected, observing whether the tip of the crankshaft extension runs out of true.
(Note for archives: in general, do not run engines with aluminium flywheels without the blade plate: they may kick back when you pull the starter. Usually engines with cast iron flywheels will not kick back strongly.)