I can understand the 3-over-2, since the cycle tended to be "Clear(green over red) , Stop(red over red), Approach(yellow over red), Approach Medium (yellow over green), Clear (green over red again)" as the train progressed through each succeeding block.
So where would the second yellow come into play? I thought maybe if the signals were close enough together a second yellow might be needed to show "Advance Approach (yellow over yellow)", but that by itself doesn't explain why a second green would also be needed on the lower head.
I'm not familiar with CNJ signaling, but from your wording about a second green or second yellow I get the impression you may have a misconception about how signal heads are normally used. That is, a single signal head does not show more than one light; in other words, green over red or any other combination would not be shown on one head. The top head would show one color and the bottom head would show the other. So, a "second green" is needed because if the top head is displaying yellow, then the bottom head has to display the green for yellow over green.
Also, railroad signals typically have vertical color light signals arranged the opposite way from highway traffic lights - that is, railroad signals typically have green at the top and red at the bottom.
