I'm not familiar with the aerogate3 (quick search shows it's a temp/fan monitor/controller?) but if it's expecting clean power from a PSU, you should regulate the car power. Also, if it uses 5V (4-pin molex carries both 12V and 5V), you would need to use a voltage step-down.
I'd ask why you're connecting it directly to the battery rather than the PSU (you do/will have a computer, right? ), but I'm sure you have your reasons.