Did your donor have cruise control by any chance. I believe the controller for this is mounted near the ECU and will add extra wiring. My engine loom came out pretty much as in the Bently manual except that there were a couple of small extra connectors next to the ECU one. that didn't sonnect to anything.
There is a good (Russian!) website that has all the wiring coulrs for the engine loom
http://www.autolib.diakom.ru:8001/CAR/BMW/ this migt help you.
Are the other wires you have all tied up in the engine loom or are they just running thru' the same hole in the bulkhead?