The alignment menu has two configuration options regarding the 3000's thermals - 1-02 TEMP and 1-03 FAN. TEMP is set to 100, FAN to 128. FAN seems to be fan speed controll, the fan is a standard 12v brushless 60mm fan (Panasonic ASFN60371) with positive/negative terminals only so the fan speed is controlled with voltage.
The FTdx3000 brochure indicates that the fan comes on at 40°C which is approximately 104°F - it's possible that the TEMP value is the temperature in farenheit where the fan comes on? That doesn't make much sense, seeing as Yaesu is a Japanese company. I intend to do some testing on this front and will update.