Eventually I tested both ways (on the same unit), with the fan inside the case blowing up/down.
Blowing down = 43C.
Blowing up (as they are shipped by BFL) = 39C.
Was this with case on or off? I've heard that it's only worth it to swap the fan if you remove the case, and run it bare. Either way, thanks!
Yes, the case was on. As long is inside the case the Jalapeno is better cooled as shipped by BFL. (fan ^)
If you remove the case OTOH the aluminium radiator (and chips) are still properly cooled, but the board and the MOS-FETs are rapidly overheating. This time you need to point the fan downward since there is no case to channel the airflow properly.