Hopefully we can get this stickied because I had to search everywhere on SHOforum to get this information.
Today I had to install an aftermarket cd player in a Gen II SHO
for Dan's (DPNovitszky) friend. I told Dan last night that they would need to stop at Best Buy to get a wiring harness. When they got there this morning, there were three harnesses, where there would normally only be two. Dan told me that the extra was for a bypass, but didn't know exactly what it was for. I wired up the power, ground, and constant leads, but didn't know which harness to use for the speakers. I went outside, and took a look at the old unit that was in there (JBL cassette). The back of the unit had the old standard Ford power harness, and had a small, squarish harness, that I took to be the speaker harness. There were also three harnesses in the dash. The standard Ford power, a standard Ford speaker harness, and the speaker harness that was connected to the JBL unit. I decided to use the standard Ford speaker harness, as I was assuming that using that harness would bypass the JBL amplifiers in the trunk. I wired it up, plugged it in, and got power, but no sound. After checking connections a half-dozen times, I took a look at the amps in the trunk to see if I had to jumper two harnesses together back there. It seemed to me that the squarish looking harness fed into the JBL amp, with another harness connected on the other side of it. Additionally, there was a harness coming from the second amp, which controls the subwoofer.
At this point, I had no idea what to do. I checked the TCCA to see if anyone knew, but neither Rudy nor Paul Nimz knew what to do. I then surfed the Audio forum at SHOforum for awhile, and saw that people were saying that you simply needed to disconnect the aforementioned three harnesses in the trunk. Well, we did that, and voila! The cd player gave decent sound from the stock speakers, and the install was all but finished.