That's a lot of dBs (1000Watts RMS @4 Ohms, @12V) in an M3!
I also have an MC4000M, MX4000 Head Unit, Empeg with 2 each 250GB PATA drives, 58F Cap & 2 local batteries. I use Boston Pro Components all around Plus 2 Infinity 12s".
The Mac can really perform well but you have to provide a low impedance power source (see Middlebrook criteria) from DC to 50kHz.
In SI, a little termination and attention to layout goes a long way. In EMC, without SI, you'll spend 80% of the effort on the last 3dB.