Hello modretro when I power my GameCube's mobo the led flashes on then off but then fan continues to run. The only mod I have made to my mobo is the removal of the special ports at the bottom of the motherboard.
I don't know how you removed the ports but if it includes cutting the pins. you may want to clean the board of any possible dust. They may cause shorts. Shorts can fry boards.
But just by the pictures, it looks okay, but maybe someone more familiar with the board enough to see if anything important is missing or looks off can enlighten this problem for us.
I removed the ports with pliers and tried wiring the voltage alt. with no avail (too small and I don't have any thing to power the 1.9v) I have no idea how to find shorts.........
So I think I am giving up on this mobo... If anyone sells a GameCube mobo with its ports removed for 15$ or less pm me or post.
don't get rid of your board I can almost guarantee it's a short. just look at where you removed the ports and make sure none of the pins are touching this could easily cause a no boot
hope this helps
Test the voltages' connection with ground. 1.9v normally has a 20-30 ohm connection to ground. 3.3v normally has almost none. It is most likely 3.3v with the light flashing like that. The exact same thing happened to me when I wired one of the memory cards badly.