My Mini had a totally propritary system so I had to replace the amp, wiring, and speakers.

In the Mini there was some kind of line level output from the head unit going to the amp but the amp itself controlled all the signal processing stuff like bass, treble, and DSP settings.

The wiring was weird also because they had a 3 way speaker setup in the front doors with the crossover built into the amp and the rears were dual voice coil 6X9s.

The Mini setup was branded as Harmon Kardon so i'm sure it is totally different from yours but the result will probably be the same. (rip it all out)

Do they have any climate controls or other extras incorporated into the head unit that would prevent you from being able to remove it ?