I think I might have made a little more progress with the front panel connector. I did a little more testing and found some interesting characteristics on a few pins.
Once again, we are looking at this drawing with the alignment notch on top, and the ground in the top left corner.
I played with the board in 3 different states. The first state was 12v stand by line receiving power, all grounds connected, but no other 12v power on the power connector.
This would be the "Standby" state.
When I did this, I had a power supply that was outputting 13.8v to the standby line. It was all I had, so I made due. In this state, I had an amber LED blinking on the power button.I found out later in the BIOS logs that the standby voltage was too high and set a trigger to blink the power button LED amber. When checking the voltages for the front panel connector, I noticed some interesting voltages changing on the pin that I have listed as "BMC?" above. The voltages would go from around .11v to 3.34v and it would bounce back and forth. Maybe it was for the blinking LED? I need to do more research on this pin.
I also noticed that the top right pin (circled in blue in the drawing above) was at 0.01v, and the pin circled in yellow was at 3.34v. These will come into play later.
The next thing I tried was powering all the 12V pins in the power connector, but leaving the board off (no jumper and not pressing the power button).
This would be the "Power on Board off" state.
I did this with the ATX power supply hooked up, but left the jumper out. When checking the voltages, I noticed something interesting. The top right connector circled in blue, was now 4.97v. And the pin circled in yellow was still 3.34v.
Next, I jumped the pins on the front panel connector (the ones circled in purple above).
This would be the "Power on Board on" state.
As soon as the jumper was inserted, the 5V pin (circled in blue) instantly dropped down to 0v. When I pulled the jumper out to shut down the board, the pin stayed at 0v. This is with all 12v pins on the power connector still receiving power. I then flipped the switch on the power supply to kill power to the power connector. Then I turned the power supply back on via the switch and the voltage instantly went back to 5v on this pin. Plug the jumper back in, the pin goes right back to 0v.
I then decided to check the resistance on this pin to ground. The pin is normally open with the board off. Plug in the jumper or push the front power button with the jumper plugged in, the pin goes to about 13 ohms. And the pin will stay at 13 ohms after that until the power supply is physically turned off via the switch on the back at which point it returns to open.
This leads me to believe that this pin might be our PS_ON line. I think we can try hooking this pin to the green wire on the ATX power supply. I am going to order a 12v Booster to up the voltage on the ATX 5v standby line to 12v so that the board has the right amount of power when the power supply is off. That way I can try to hook this front panel pin to the PS_ON line of the ATX power supply to see if I can get the power supply to turn on and off with the power button automatically.
I also tested this pin when in Windows 10. With Windows 10 running, the pin is at the 13 ohms. When you click shut down, Windows will shut down and shortly after the pin will go back to open. Just another reason I think this might be the PS_ON pin.
The other interesting thing I noticed in this state is the pin circled in yellow. When the power supply is turned on and the jumper is out, the pin has 3.34v on it. Wait about 15 seconds and the voltage drops to 0.11v and stays there. Wait another 30 seconds and the voltage goes back up to 3.34v. It may be a coincidence, but about 5 seconds after that and the BMC LED begins to blink.
As soon as the jumper goes in, the pin goes to 0.11v. Take the jumper out and the pin goes back to 3.34v. I need to do some more looking into this, but I found it to be rather interesting.
I still have yet to figure out how to get the 2 on board SATA ports working. I have tried the jumper @Wictar
suggested. I will continue to try and see if i can get them to work. I am also going to order the connectors, 12v booster, and pins that I need to try the standby/PS_ON idea.