Hopefully this post isn't dead, yesterday I tried installing my alpine amp and sub and I have everything wired correctly but I don't know how to do the wiring with the pre existing amps from the shaker 500 system. My mustang is an 06 with the shaker 500. I'm also confused on what line out converter to buy because I thought I would be running this into the back of the head unit. I've kept everything stock just like you but I just need help on this final part. If you could help in more detail because I would really not want to pay someone to finish the last 5% of my install.
Search this forum, there are posts that show which wires you need to tap into.
I tapped into one coil ea. of left & rights to get a stereo signal. I tapped into the output of the Door subwoofers, just as the wires exited the door sub amps (in the driver foot well, laterally).
I chose the AudioControl LC2i line-out converter, it works exactly as advertised. The optional remote knob was perfect.
This type of line out converter allows the 'modes' of Shaker500 sound (Driver/All/Convertible) to come through, despite amplification.