Ok, I spent some time with the AFS motor disassembled tonight and think I figured it out. There is another AFS thread on here that has the same conclusions, but the wiring colours are not the same. So I am going off of wire colour, and pin number.
*x* is the actual spindle, and the connector is the pins. So looking at the box, with the connector on the right, pin 8 is on the far right.
Pins 1, 2, and 3 have 9.8ohms resistance between them, meaning they are the coils.
1: Coil A [Red]
2: Coil B [Blue]
3: Coil C [White]
4: Top Hall Effect Sensor (A) [Red]
5: Bottom Hall Effect Sensor (B) [Blue]
6: Middle Hall Effect Sensor (C) [White]
7: Ground [Black]
8: Power [Red]
The PCB is a dual layer board, and the bottom is glued/stuck to the casing, so I am going blind on the bottom of the schematic. However, my motor has 8 pins, and 6 of them are matched pairs in location. I can confirm that the hall effect sensors are correct as they are routed on the top layer. The first 3 pins disappear into oblivion, but going on logic, they would coorespond to the coils the hall effect sensors wire's colour correspond to. So the coils are guesstimations as of 07/12/08.
There is a huge amount of gear reduction in the motor, and a little bit of grease, so be careful when you take yours apart. Also the spindle, all all 3 of the gears come out.
I was a little disappointed that the gears are plastic, not what I expected from a Lexus. I can see these failing easily.
If anyone is interested I can post some pictures too, I just need to find my camera.