Quoted from maffewl:
Well, there goes that. I was hoping my RFM was fixed and bulletproof, it thought otherwise. The boot issue is back again. It freezes at the last blue line on the white screen, something about "Starting Update Game Rom" or similar. Sometimes it just freezes, and sometimes it re-boots itself. In a couple rare instances it will start the game, then boot itself.
As mentioned before, I've replaced the PSU, CPU fan, and the 5 common problem capacitors. My friend has a SWEP1 and let me use his computer to narrow down the issue, and I've narrowed it down to the motherboard. I've altered and replaced everything else. Any thoughts on what to check on the motherboard?
Im not sure if this is helpful or not. But the stock update procedure was to use a serial port. You said your system hangs during the system boot when checking for update. (If it gets this far, it has booted most the way and gotten past the typical computer issues with bad board caps etc). If when your computer lost its initial settings, the configuration of the serial port got messed up in the bios, perhaps the system is having problems checking the serial connection for update due to that.