j3 doesnt seem to function with the aux input......j4 has all the hardware for the aux/mp3 hook up. do you have anything plugged into j4?
ill look over the diagram you posted and hopefully will have more to say later. im buried in work right now. I just recently wired up a 05 mustang head unit. although it wasnt the shaker 500 system. maybe you dont have all the correct hardware on the car to swap over to the shaker?? not sure. if i were you i would put in the shaker 500 system and get an aftermarket headunit and skip the head ache. plus with an aftermarket unit you have a usb port to play mp3 players on so you could charge your ipod while listening to it.....thats what i havein my 98 .J4 appears to be wired to the sub woofer amps. When I leave in unplugged the SW don't work, and the wire colors are the same at the head and the amp.
Another possible clue is J3 pins 15-16 are "MS CAN A" and MS CAN B". They are the only pins connected in the stock (2005) configuration.
Bumped thread. I am still looking for an answer.