Soft fade out circuit for turning off speakers
OK something is missing here... If you turn off the pre-amp there should be nothing to fade... at the amp. Further, the pop is caused by the transient of the pre-amp shutting down, and is short, so by the time you fade out the amp it's too late. 

Since they are powered separately in different boxes I think you need to make the AMP mute the output when the pre-amp shows it is off. There may be a way in the pre-amp to fade out before it sets the shutdown line though.

I'd be interested to see if that line from the pre-amp really "immediately becomes 0V when preamp turns off" or if it actually fades out with the preamp power supply. It it's the latter you could use that to turn off the input more gracefully than a relay.

Perhaps with an LM13700 Dual Operational Transconductance Amplifier wired as a unity gain voltage controlled stereo volume control between the pre-amp and the amp. RC shown here would need to be adjusted for your output signal from the pre-amp