The first picture looks like they had some kind of audio device that was hooked into the black connector (that almost looks like a headunit connector). I see an orange wire (dimmer), red wire (constant +12v), black wire (ground) and a hint of a yellow wire (switched +12v), the RCAs are line-level outputs. I have no idea why it would be in the trunk though, unless they kept the HU in the trunk (edit: Unless i'm mis-interpreting the first picture and it's your passenger foot well and not the trunk)- this type of harness is typically kept in the dash.
The speaker wires connected to the crimp connectors are the front left (gray, black/gray) and rear left (green, black/green). I don't know why they'd be connected to the factory wiring harness though (the pink and blue/yellow wires)... is that a Honda?