There is an external GPS receiver box, also called the "Trimble Module" that you need to remove. The Trimble has the little coax antenna plug on it. Disconnect the trimble, and then reroute the antenna cable over to your MKIV.

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2000 E38 750iL Highline Edition, Upgraded with the lastest 2006 X5 Electronics
MKIV Navigation, 16:9 Display, Bluetooth, TV/Video with Backup Camera, Sirius, and Aux Input