Are there any parts of that which will be particulary gnarly that will need fixing first?
Count the number of external interrupts you can have on your particular Arduino. I think that you will find that you do not have enough.
Does the pump actually have a way to measure it's speed? Does the pump speed really matter?
For that matter, do the fan speeds really matter? Either they are going fast enough to cool the PC or they are not.
The case should only cool what it needs, not go flat-out 100% of the time.
Maybe just a simple ripple-counter. Might still use a lot of pins though.
Does knowing that one fan is spinning 7104 RPM while another is spinning 6519 RPM matter? If not, if you just want them all to go faster or slower, then all the interrupts needed to read the speed are not necessary.
If the speed of any fan/pump is particularly high, and I imagine that they all are, you will need to detect speed using interrupts. Each time the fan/pump outputs a signal, an interrupt handler needs to be called to record that fact.