Because the Babbitt in the block was so woefully worn, I suspect the crankshaft now sits a little higher inside the block, which would increase the backlash between timing gears. I installed the largest oversized fiber timing gear available because the friend didn't want to spend the money to have the main bearings re-poured. The .005" oversized timing gear reduced the backlash to around .006", which is not ideal, but most certainly softened the clicking/knocking to barely perceptible.
If you didn't check this area, that may be the cause of the elusive knock.
Marshall