Hi again,
wow you're in the wars over this and I really feel for you. I would be really surprised if it is the motherboard but that doesn't mean that it isn't. When I am faced with this kind of situation the first thing I do is go back to the beginning and build the PC on a cardboard box with as few components as possible.
Removing the motherboard from the PC Case, eliminates the possibility of it shorting. Before you reconnect the power leads it is also a good idea to clear CMOS properly, just in case it has become corrupted.
Put the basic components together, CPU, Cooler, 1 stick of RAM and the GPU and the keyboard, plus the mobo speaker and power and reset switches from your case (if you don't have a separate test kit), then try and power up. If it still doesn't start properly, remove the graphic card and see what POST Beeps you are getting as that could be causing a problem, especially as you say you are getting red leds showing on it. Do you have another graphics card to try?