Very good point about the pinout, I forgot to include it. Also The file system had not struck me until this moment. However I am not sure if this makes any difference but the ipod works as a mass storage device under windows when you connect it with either usb or firewire. So I assume and may be I do incorrectly that it should already be good to go, there may be some weird apple os spot on the drive, which I can use either linux or some partioning program to clean off.
Unless of course for some weird reason the ipod was able to adapt some weird file system so windows could read it with the use of electronics or some other such way through the ipod (make windows think it can read it, but allow the hd to have some weird format) I am very familar with linux SO I could use it to format and part the drive If it came to that.
Here are the two pinout tables I am using. I am pretty sure they are correct, Unless anyone wants to add anything. I tested the pinouts on my drive and Was able to get the drive to kick on, which must mean the pinout table matches up, The pinouts are for the 40gb drive for the Ipod, but it uses the same connector, and I see no reason why it would not be the same for mine. or for all ipod hd's for that matter.
Also here is an image of the pin assignments for the HD: