As for models of coolant pumps, I'll leave that for Steve or anyone else here.
Looking at your user name and our order history I'm guessing that you have a PMDX-126, correct?
There is a separate, dedicated EStop input on the PMDX-126 on connector J13. Your EStop circuit should be connected there, between the "E-Stop' terminal and the adjacent "GND" terminal if your EStop switch is normally closed, or between the "Fault" input and the adjacent "GND" terminal if your EStop switch is normally open. We DON'T recommend using normally open contacts for EStop because if the wiring comes loose or breaks somehow you will never know it until your machine DOESN'T stop when you hit the EStop switch.
For your limit switches, it *is* possible to wire them all in series to a single input on the PMDX-126. However, if you do you will have to enable "limits override" to jog off any of the limit switches since Mach3 can't tell which limit (positive or negative, Z, Y or Z) was tripped.
Will any of these also be used as a home switch? Do you have any other input signals that you need to connect, like a touch probe? If you also want to use, say, the minus limit switches as home switches, we usually recommend wiring each limit/home switch to its own input. You can then gang the three positive limit switches to the 4th input. With this arrangement Mach3 can home all 3 axis at the same time. Not necessary but a little quicker.
If you also need a touch probe or some other input signal, you have a couple of options:
(1) Wire all 3 negative limit/home switches to one input, all 3 positive limit switches to a second input, leaving 2 inputs available for other uses. Mach3 will have to home 1 axis at a time.
Or...
(2) Use "Expanded Inputs" mode to give you 8 inputs instead of 4. The drawback to this is that if you have the "charge pump" feature enabled on the PMDX-126 (which we recommend when connected to a PC's parallel port), you will not be able to see all 8 inputs when Mach3 is disabled ("Reset" button is flashing). They will only be available when Mach3 is enabled since the charge pump signal is used to multiplex the 2 sets of 4 inputs into Mach3.
Bob