Most E-stop switches has two contact blocks. Usually one normally closed and one normally open but it can be two normally closed ones. You use the second switch wired between GND and an input on the break-out-board to tell Mach3 that there's an E-stop.
Normally it's not considered safe to wire the E-stop as you have done. It should not be enough to simply release the E-stop for the machine to start up. What you normally do is wire up a relay and a pushbutton so that the relay activates and latches with the press of the button. The E-stop switch is then wired in series so that power to the relay is cut off when E-stop is pressed. That way you have to release the E-stop and press the pushbutton to enable the system again.
As for the fans, get two 24V fans and wire them in series across the 42V supply. That's proably cheaper than getting a separate supply just for the fans.