Your box is an amp but it doesn't have the conventional sub hookups because it is specifically made for your car and uses special harnesses. Usually there are 2 amps, one silver, one black bolted to the back of the seat behind a cover panel. Black is for the 6 1/2" sub bolted in an enclosure under the middle of the rear deck. The silver is for the rest of the speakers.
Now your harness is indeed for a factory CD changer. The changer went in the little depression in your trunk on the driver side between the rear wheel well and taillight panel. The changer has a wire and plug that runs up the driver side behind the trunk trim panel and connects to that harness. Controls for the changer were standalone from the JBL head unit and used a special harness to connect to the cassette player.
Configurations for your dash/console for the radio depended on your system. There were 5 options on the SHO:
#1 - regular am/fm cassette (no AUTOMATIC on tape deck door)
#2 - JBL am/fm cassette (all JBL had AUTOMATIC printed on tape deck door)
#3 - JBL am/fm/cassette/cd
#4 - JBL am/fm/cassette/6 disc cd changer
#5 - JBL am/fm/cassette/cd with digital graphic equalizer
#X - JBL CD only (rare or pirated from another ford/lincoln/mercury/ebay - single cd player where cassette would be)
#Y - a plain old am/fm (rare)
#Z - no radio at all (rare, harnesses still there but a radio delete plate covering the slots)
If you had #1 or #2, you had the head unit in the first slot, then either a coin/cup holder or fold down storage compartment in the bottom slot, and a cassette caddie and cigarette lighter insert in the console right below the slots.
If you had #3, you had a cassette in the first slot, cd addon in the second slot, and the cassette/lighter console.
If you had #4, you had a cassette in the first slot, the coin/cup/storage in the second, and changer controls where the caddie/lighter would be.
If you had #5, you had cassette in the first slot, cd in the second, and controls/screen for an equalizer in the console.
You can mix/match any of the Premium/JBL/Mach 460 system components except Premium/regular cannot connect as the harnesses were different. Hope that helps.