That all looks good; but you may have some trouble using BMW's antenna with your computer's FM tuner. Some have reported success with this; for me it doesn't give me any improvement. I just strung a normal FM dipole antenna across the top of the trunk and it works better than using BMW's OEM antenna. Still it's worth trying.
Those cat6 cables would be good if you wanted to hook up some serial devices or something, so I think you have the right idea with that. I actually bought serial extension cables; I don't know what I was thinking. I have a big bag of like 50 RJ45->DB9 hoods!
Instead of burning one of the wires in the cat6 cable for your shutdown controller, why don't you just run an extra pair of that 18-2AWG cable? or a single spare 20-24 guage wire? Since you're running the cables all anyway might as well not waste that spare cat6 so fast...
And yes the black wire on the SVEN4 needs to be connected to the GND in the radio wiring harness in the front, but it should be the same GND you can attach to anywhere in the car or by screwing to the chassis. See, the amp wiring in the E46 is balanced, so it's actually 3 wires per speaker: Signal +, Signal -, and GND (GND is shared between all 4 speakers) This is unlike unbalanced audio which will have only a signal and GND (but often the GND is isolated) Since this GND wire is a vital part of the audio path I would not recommend putting it through on a piece of cat5. The wire is not big enough for one and the potential for noise is greatly increased. I would put the entire SVEN4 up front. Run unbalanced audio from your computer up to the SVEN4 through your coax then connect the balanced audio out of the SVEN4 to the wiring harness in the front of the car.