Does your blu-ray drive still work on the new motherboard? I seem to recall on the PS3 that the blu-ray drive was tied to a console, I assume you had to reformat the HDD also?
This is untrue. Over time thermal paste will dry up and crack and not provide good coverage between the device and the cooler. The paste massively improves the thermal transfer between the chip and the heatsink. If you do not believe in the magic paste then you should wipe it all off and apply just a little bit or none at all and then compare temperatures. You will see the paste is responsible for a big reduction in temperature.