I got the call from the Apple store this afternoon that they had fixed my Macbook Pro again. They were gracious enough to admit that the problem with the fans due to a mistake when installing the new logic board. As I suspected, one of the temperature sensors had not been pushed home properly and so the fans were running in their default safe mode, so it was definitely worth getting fixed.
Just a few hours of work to do now to restore all of my data and programs (again).
Lets never speak of this again.
