I did several searches for this type of problem, but didn't find anything similar although there are some other types of clicking issues.
I haven't pulled the gearcase again, but I did rotate the agitator by hand and could hear the clicking sound. It occurs at 8 o'clock and again at 2 o'clock (180 degrees apart) when rotating the agitator clockwise. There is also a very very light sound (almost a feel) in the agitator near the same spots when spinning it counter clockwise. It sounds like a little metal piece being pulled back and then "clicking" past whatever is pulling on it when turning the agitator slowly.
Anyone have additional thoughts on this? One would think others would have ran into this issue with re-assembling a gearcase and washer.