Hahah, wow that's pretty ridiculous. I do have an extra wiring harness that is part of the wiring harness that hooks in to the amp. I think it's like a 6 pin and then a 4 pin - probably has something to do with the 6 cd changer (which I don't have). Weird that out of the only wiring harnesses they left in, that was it.
Well I did search this site and some of the other e46 forums, and it seems most of the people who tried doing this gave up, or used a DIY site on EarthLink that has been down since 2005!
I suppose just taking the wiring diagram to the 10 pin on the pre-amp is enough to figure it out. And I am going to guess that the 2 pin plug probably goes from the left speaker (the one with the pre-amp) to the right speaker for the power; i think the right speaker has a separate signal.
If I can figure this out i'll post back on here. Thanks