Reading the rpm of multiple fans
If temperature regulation is what you seek, why bother with the Tachometer signal at all?

Thermistors don't require interrupts. Why do you need fully closed loop fan control? A simple proportional control of each fan and each hot item would likely suffice in keeping your system cool. Noise concerns, perhaps?

A brief article on proportional temperature control

A data sheet on a TI chip that may have some inspiration for you