The shaft does not come out, you just pull the propeller out and the disk just sits on the shaft concave end facing the propeller assembly. It is best to dissassemble it as the vinegar doesn't tend to penetrate all areas otherwise.
On a single controller with y adapter both pumps mirror each other, they will both do the same thing. Night mode is whatever the bottom speed knob is set to.
The SS disk is a new part and was not in the manual that was printed some months ago, it is basically a very tiny washer. The manual describes a nylon disk which is still present, this one sits on top of that, between the nylon disk and the prop magnet.