On the D16Z6 5-speed tranny there's a bolt located near the shift rod under the differential gear. When you open it there's a spring and ball located in it that rest against the shift rod. Can anyone tell me what they're for and exactly what they do? I don't really see what they're there for. Obviously they work with the shift holder, I just dunno how they do it.

It's parts #21, #11, and #16 in this link:
http://www.hondapartsnow.com/online/...se&ScrollBar=0

 

helps hold the shifter in gears.

Forward/Center/Rearward

 

they called detent *****.
they are some of that 'notch' you feel when shifting

 

detent ***** keep the gears from poping out