Thanks David. When I remove it again I'll check it using the procedure in the manual.
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I tested it again this morning to check linkage ( i.e. Does moving the shift selector cause any change in the deceleration noise). It didn't.
However, I focused on 3rd and 4th gears again today, and I really don't hear the same noise in those gears. I think the faint noise I'm hearing is residual noise from whatever gear is messed up, like I'm hearing in neutral. Therefore, I don't suspect the bearing preload or the spider gears anymore.
So, the noise is really focused on 2nd gear. Which makes sense because when the nut-backing-off event happened in November, I tried to get it in gear after stopping at an intersection, I wouldn't go into first, but it went violently into 2nd. That's where the shift selector damage happened, but perhaps something also happened to the 2nd gear assembly. Something internal as the gears looked normal and I didn't take the gears apart, and the 1-2 selector fork appeared straight.
What would be the symptom of the 2nd gear synchro spring (103106) being broken or damaged?