There are indeed two different types of 17" iMac G4 necks and the wire color does vary between them.
1) Part # 661-2716. This neck comes from the 800mhz 17" iMac
2) Part # 661-2825. This neck comes from the 1Ghz and 1.25Ghz 17" iMac
I am fairly certain that my neck came from a 1.25Ghz machine, so those modifying a 1 or 1.25Ghz iMac should be able to use the pinout I have posted. However, those modifying an 800mhz will have different colored wires.
As of right now, I would still recommend opening up the monitor and looking at the JAE connector and following PIN NUMBER instead of WIRE COLOR. As the LCD panels are the same the pin number will always be correct.
I am trying to obtain a completely intact version of each of these necks to detail the differences and will post the differences when I do. Several people have gotten this working, while others seem to be having some trouble. I will try to go through this step by step and post detailed instructions of how t connect this. I will also try to do it using a spliced DVI cable as most people seem to be going this route.
I am also working on the step by step for the cinema display 20" mod for those interested in doing that