Unless things have changed dramitcally since I last had a Pioneer head unit/autochanger the power and earth connections used to be connected externally to the bus cable (very thin wires as it pulls little current).
This means that effectively you run one cable from the head unit to the autochanger foe ease of installation.
Pioneer looms also have a secondary power connector capped off, to plug this part of the autochanger cable straight into.
Rather than fanny around in the boot looking for a suitable switched supply, or mess about with relays and remote wires to create one, I would simply run new wires and connect them into the back of the head unit (make sure you use the accessory switch power supply, not the permanent, or you'll continue to have the same problem).
Thinking about it, you said you have two remote wires terminating in the boot that used to power amps....are these no longer used? If so you can use these, just disconnect them from the remote wir from the headunit and connect to power and earth.
