Hi Dark Mantis,
I finally got to the bottom of it and I have a working computer once again.
I had two problems.
First was my waterblock had lost contact with the CPU and simply wasn't cooling it, so the CPU was protecting itself and shutting the machine down. Having started again with some fresh Arctic Silver the machine is now running reliably and cool again. I feel very silly about this, though it's strange because the waterblock (Apogee XT) is bolted down with 4 screws and is under spring tension(!) Unless it was unevenly mounted...
Secondly, one of case's USB ports has become damaged and was shorting out. This was causing the board's rapid power cycling earlier. I've unplugged it and will repair it later
Unfortunately to add to my frustration the graphics card nearly died too! I was getting artifacts even in the BIOS screen. Because of XFX's poor warranty policy I had no warranty cover due to fitting my EK waterblock.
So instead I used a hot air reflow station to repair the card myself, and now I have a working card. I enjoyed a full evening of BF3 last night!
I'll probably retire it to being a spare and buy a new graphics card in case the repair doesn't hold out, but this time one with a warranty that allows for aftermarket coolers.
What a frustrating week, but I got there in the end. Thanks for your support!