With respect to the tach signal:
- The tach signals on these fans are an open collector output. You will need a transistor to simulate that.
- PWM pins on the Mega are 490Hz. Assuming wiring is correct then the RPM at the main board would be interpreted as 490*60/2 = 14,700. Doesn't seem a reasonable RPM.
With respect to the PWM it looks like it should be around 25kHz. The way you have it programmed you will be getting 50 interrupts per millisecond.