You mentioned the VGA board fan PWM had stopped working, so I would not trust the software reported fan speed.
To verify the damaged PWM, connect the fans to the VGA card and at idle the fans will be slow and quiet and under stress, fast and loud. Make sure to turn off any software fan profiles.
The fans can be connected to the power supply and run 100% always.
The fans can be connected to a fan controller and manually adjusted.
The fans can be connected to a 10k rotary pentiometer and manually adjusted.
I would add that the Gigabyte heatsink can cook a higher wattage than the Asus because of It's size. Therefore, I would bet that the broken fans also blow more air than the replacement fans. Just compare the size, number of blades, the thickness of the fan, and the amperage and know that the bigger compared item will move more air.