I don't know why I didn't say this before. If you're putting components in, just run two wires to the HU from the battery. Connect one to the HU's power wire. Run the second wire to a toggle switch, then to the HU's ignition wire. This way you can manually turn the HU on and you won't clear the HU's memory when you shut it off. Then just ground the HU to the chassis and you're good to go.
Since you will be using aftermarket comps and a standalone amp, there is really no reason to use the factory wiring. The only wires on the factory harness you would use would be the power and ignition (since you have to run wires from the amp to the comps anyway). Plus you'll get a better power and ground with dedicated connections.