Hey 01path,
The manual does not list the color codes for the wires (that I can tell anyway), instead it goes by pinout number. So to map between with-Nav and without-Nav (pinouts on mid-pg HA-40), you have to look at the wire position in the connector, and look up the purpose of that wire in with-Nav, then find the wire with the same purpose in without-Nav and pair the two. Almost all of these pairings share the same colors. But there are some that either do not, or no longer have a purpose.
Example - your picture below looks like the with-Nav plug:
Pin 9 Grn/Wht/Sil is "Sensor Ground" (pg. HA-42). It pairs to the wire on pin 11 on the without-Nav plug (pg. HA-40).
Pin 10, Grn/Red/Sil is "Sunload Sensor", and pairs to the wire on pin 12 on the without-Nav plug.
Follow this system to determine the purpose of your leftover wires, and see if there is a corresponding wire purpose in the without-Nav plug.