Curious. My business Nav was simply a BMW HU with 17 pin connecot and a MK3 in the boot with all nav stuff done over the 1 wire navbus.

The problem you will find is that all BMW harnesses start off with an 8 pin connector near the front fusebox. This then supplies power, GND, iBus and illum to the various boxes in the car (dependig on options fitted). This then feeds the speakers.

Your system will have the radio connector in the boot, and the speaker connections will run from there.

Your choices are
1) Rewire the car (all the way to the doors) with a factory install (not retrofit) harness (for 16:9 nav or 17 or 40 pin up front)
2) build an extension cable for a 40 pin to 17 pin cable out of some SOT adaptors (eBay) - note the female and male 10 and 12 pin plugs are impossible to get hold of.
3) Get a DICE mediabridge and use an iPod