the 4-pin molex connector would be for powering external components (monitor, USB hub, HDD, etc). as long as they retained the standard ATX wire colors; yellow= regulated +12v, red= regulated +5v, and the two black wires are ground.
judging by the last pic, the other 5 wires look like they are plugged into:
J1 - thick RED= 12v constant power (car battery)
J3 - thick WHITE= switched 12v power (ignition switched)
J4 - thick BLACK= ground
J6 - thin RED looks like it's the delayed AMP turn on wire, and I'm not sure what the thin BLACK wire goes to (maybe the ground pin on the J6 header?).
DON'T ASSUME that the wire colors are standard. the previous owner could have wired it different from what the pics show. before you hook anything up, you need to open up the case see where each wire is connected to. you can view/download the M2-ATX user manual here. page 2 shows power inputs and where each wire should go.