*UPDATE* Just fixed the issue. Apparently the reason the fan revved up then shut off was because the thermal paste couldn't contact the heatsinks from the CPU/GPU. (Had to disassemble up to Step 28)
I looked around and found this thread:
Heatsink doesn't make contact with processors
However, even after filing the heatsink's "ears" for a while and putting folded paper under the clamps, I was barely getting any paste on the heatsink (and I was running out of paste). So I simply applied the paste to both the processors and the heatsink whilst still adding pressure to the clamps.
It's working like a charm now, fan was near silent for the first 7 or so minutes, now it's running normally.
I'm having the same issue. After a few seconds, the fan gets really loud, I get a message saying that the system is overheating, then it shuts down.
I remember clearing the fans of dust when I had disassembled everything...