My computer has developed the "blinking box" syndrome

You'll need to give more detailed hardware specs of this custom rig, and also how old the parts are that you're using as well as how far you overclocked and what kind of cooling is available to the machine. It's possible that you simply stressed the motherboard and/or memory too much and it ended up corrupting some data, causing your drive to acquire a fault. That's total conjecture but without further details noone can help you.

Hmm, maybe you need to reset the BIOS. I have had that happen to me occasionally (crap BIOS, no overclocking) and sometimes it just goes crazy. I'm sure someone else will chime in with other suggestions; again, it's just a theory.

Jam it back in, in the dark.

See, I think it might be corrupted. I have this annoying problem with my system (which is supposed to be a server-class motherboard, also an ASUS) where if I get a BSOD or a freeze, and then hit the reset button, it corrupts the BIOS and I need to go into it and quickly adjust the settings back to how they should be. I need to do this a couple of times before it'll stick. If I just hold the power button down for a few seconds and shut-down that way, it reboots normally.

Numerous updated BIOS versions haven't fixed it so I just live with it. Fortunately my system rarely hangs. If you can boot from your motherboard CD, the built in flashing tool on the motherboard should be able to copy the BIOS file onto the CMOS chip without a problem, but i'm sure I don't need to tell you that :P.

There's nowhere I can't reach.

Is your RAID mirrored or striped? I was gonna say if it was mirrored, just use one drive and plug it into a normal controller (unless it makes no difference - some motherboards have dedicated controllers attached to only a few of the SATA ports for RAID purposes).

How ya doing, buddy?