After much messing about (I really need to get a bigger case!), I just got the whole motherboard out and took off the PWM heatsink and also the northbridge heatsink.
On inspection, the PWM heatsink is actually very concave(!), measured with a straight ruler, there is an alarming gap in the middle. This also resulted in less than favourable contact on the middle sets of chips the heatsink is supposed to cool. Unfortunately, I don't have any sandpaper right now to lap (and nor do I really want to) and so a new layer of Arctic Ceramique was applied, with a thicker bit for the middle so that more contact could be made.
At the same time, the northbridge heatsink was reseated as was the cpu waterblock.
Everything was put back into place and with great expectations, I fired it up and started priming away.
The short of it all is that the PWM temp is now 113C (!), which is still very high, but better than 124C, a drop of 10C. As for the CPU, it now reads: 54/50/55/55C across all four cores. (I don't know why core 1 is so low, it was like that before too) This is after Priming small FFT (max CPU) for about an hour (still going), again at 378 x 9 = 3402MHz, CPU-Z reading of 1.320v (1.415v in BIOS).
To be honest, I'm not really sure what to do next.
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