I've got an older atx 1.3 power supply running slightly newer equipment. There is a 6-pin aux connector that the motherboard doesn't need are there any adapters available that could turn it into a 4-pin molex or two.
I don't think so. I rummaged around in my junk box and found an old ATX 1.3 PSU. The connector you are talking about looks like half of an old AT PSU (flat white connector that looks like it mates with flat pins, right?
The 6 pins are:
3 black - ground
2 orange - 3.3 volts
1 red - 5 volts.
12 volt output is not available. If you need to run another drive, buy a Y-type drive power adapter (molex female to 2 molex males).