As the others have mentioned...
Cradle, fuel pump, throttle cable and gauges.
ECM and engine harness. The harness unplugs from the block next to the battery. The V-6 harness plugs in, in its place. You'll need to swap the red wires, too.
The A/C and fuel pump relays are all part of the engine harness.
Your fuel lines already enter from the right side. You just need to connect the hard lines from the fuel rail to the flex lines that come from under the battery tray.
The 86 water pump has a pipe fitting that points toward the trunk. Remove that pipe fitting, and screw a pipe plug in the hole. Do NOT just put a rubber cap over the pipe fitting. It'll blow off. Seen it happen.
The Duke has a water hose that connects to the bottom of the intake manifold. From there it goes to the right side frame rail and down to the heater pipe. Remove it from the car. It needs to be replaced with a pipe/hose assembly that goes up the right side of the firewall and over to the thermostat housing. All 87 and 88 V-6 installations use this hose.
Important! If you're going to retain the A/C, look at the drier canister in the front compartment. Make sure the low pressure switch is installed on the shrader valve. If there isn't one there, you'll need to install one. This requires replacing the heater fan/windshield wiper wiring harness.
Not a big deal to do, but if you *don't* do it your compressor can still kick in, even if there is no refrigerant or oil in the system. Will turn a compressor into a doorstop in very short order. Don't ask me how I know this.
I may have forgotten something, but that's most of it.
88 3.4 coupe. 17s, cut springs 'n all.