I just looked under my playfield and I can't find that type of 9 pin anywhere.
I do have a open 9 pin straight inline IDC connector up near the TYFASSI Flipper board. I'm assuming it is used to Imports or a different flipper board.
As for the hook lights, under the playfield where the Z connector is you will have coming in the 3 orange wires which select the 3 different light strands (by going to ground in that chase module), and the one grey wire which is the common +12V to the lights.
DSC01132.JPG
All 4 come down from that Z connector in the backbox. (Along with the 3 other wires were have no idea what they are used for and you have missing)
The three orange ones come from the chase board, they get their 3 inputs from the re-purposed 3 outputs off of the CPU that would have been for a segment display off of CN3 Pins 7,8, 9.
The +12V (Grey/Wht) wire come from the P/S off of CN6-3. According to the picture of the P/S in the manual, CN6-3 is +12V but there it shows N/C (Not connected). So that is a documentation bug.
DSC01142.JPG
The lights are not timed/random but driven off the game. What happens is you should always have 12V on the grey/wht wire. The CPU then sends out one of 3 signals off CN3 that tell the Chase board to ground its corresponding line. 12VDC on one side of the rope light + ground on the other = lamp on.
If you have +12V at the chaselight connector, you should be able to dissconnect the orange connect off of the chase board and ground each one at a time and light up that section of the rope light to prove continuity from the chase board all the way through the rope.
DSC01133.JPG