here's a tip from a Honda manual..
"Check the condition of the big-end rod bearing by grasping the rod in one hand and lifting up on it. With the heel of your other hand, rap sharply on the top of the rod. A sharp metalic sound, such as a click, is an indication that the bearing or crankpin or both are worn and the crankshaft assembly should be replaced."
This test was done on a crankshaft removed from the engine but the crank is still attached. This way there's no mistaking a main bearing or a wrist pin problem for the big end problem.. The only thing that could "click" if the crank is removed is that big end..
In your case, try this.. just remove the head, turn the crank until the piston starts on it's down-stroke. Now the rod and bearings are "stretched" out .. Hit the piston's top with something soft that won't make a noise.. maybe the heel of your hand is enough.
The only wrong with this method is that the wrist pin could make the clicking noise, or perhaps the main bearings.. But its six of one and half a dozen of the other.. ANY clicking noise is gonna be bad newws.