BMW E46 3-series help!

Well to start off my system specs are located in my sig. and I had an audio shop do the installation and after a few trips back and forth to have the fix what the screwed up I decided to rip the entire system out and redo the install myself. This isnt the first time I've had to correct an audio shops mistakes.  To get to the point I am running new speaker wire to my doors and I've come across a bumb in the road.  I've come to notice that BMW builds their cars well, very well, because instead of the wireing harness simply going through a simple hole and through a rubber grommit type thing and into the door, BMW decided to make the door harness connect to the chassis with a plug.

The question:
What has anyone done to run new wires through this?  I was going to cut the wires that connect to the plug and just attaching new wire to the exhisting plug but then what is the point of running all new wire anyway.

I hope you guys can understand what I am trying to say, and can visualize what I am.  If you need more clarification please ask.

Thanks for any help you can offer.  
-2 JL 10 W7v2
-2 JL ZR650 CSi
-2 JL 500/1
-2 JL 300/4
-JL Clean Sweep
-600 Farad Cap.
-ESQ 6 Ch. Equalizer
-Ground Loop Isolators

All packed in the back of a 2006 M3 Competition Package